Early in the colonial period, men formed the first notable government that legally protected separation of church and state and religious liberty. This historical event arose out of a conflict between the two currents which flowed in opposite directions.
“A large number of people fled out of the old world into this wilderness for religious liberty; but had not been here long before some put in high claims for power, under the name of orthodoxy; to whom others made fierce opposition professedly from the light within; and their clashings were so great that several lives were lost in the fray. This made a terrible noise on the other side of the water. But as self-defence is a natural principle, each party wrote volume after volume to clear themselves from blame; and they both conspired to cast a great part of it upon one singular man [Roger Williams], whom they called a weathercock and a windmill. Now let the curious find out if they can, first how men of university learning, or of divine inspiration, came to write great volumes against a windmill and a weathercock? secondly, how such a strange creature came to be an overmatch for them all, and to carry his point against the arts of priestcraft, the intrigues of court, the flights of enthusiasm and the power of factions, so as after he had pulled down ruin upon himself and his friends, yet to be able, in the midst of heathen savages, to erect the best form of civil government that the world had seen in sixteen hundred years? thirdly, how he and his ruined friends came to lie under those reproaches for a hundred years, and yet that their plan should then be adopted by thirteen colonies, to whom these despised people could afford senators of principal note, as well as commanders by sea and land? The excellency of this scene above those which many are bewitched with, consists in its being founded upon facts and not fictions; being not the creature of distempered brains, but of an unerring Providence.”
Many brave men and women, with Baptists at the forefront, paid a high price on the path to religious liberty and freedom of speech, association, and the press. One should not forget that those people were motivated by a deep love for God and his word, not by earthly concerns.
As a result of the fight, Christians, and everyone else in America, have religious freedom. The United States Supreme Court still upholds the wall of separation between church and state and freedom of conscience.
Christians in America have been blessed above measure and can choose to please God and not be persecuted for it. The brief time men will be on earth is miniscule compared to eternity. The time an individual Christian is here is nothing more than a blink of the eye. An American believer now has the opportunity to glorify God without persecution. That opportunity was the result of the trail of blood left by the martyrs for Christ.
Every breath a believer takes out of God’s will is a wasted breath. He will praise God naturally, not as a matter of choice, in heaven. This is his one chance, during his eternal existence, to live for Christ of his own free will. This is the one shot he has to choose to please, serve, praise, and glorify God. After leaving this world, some will learn, when it is too late, that they never glorified him when they had the choice. Some will learn that they did not proceed according to knowledge, understanding, and wisdom; and that they followed and promoted the principles and goals of the god of this world.
 Isaac Backus, A History of New England With Particular Reference to the Denomination of Christians called Baptists, Volume 1 (Eugene, Oregon: Wipf & Stock Publishers, Previously published by Backus Historical Society, 1871), pp. 408-409.
 See Jerald Finney, God Betrayed, Separation of Church and State: The Biblical Principles and the American Application (Xulon Press, 2008 (www.xulonpress.com), Section V. Sadly, while upholding that wall of separation, the Court has also twisted the meaning of the First Amendment so as to remove God from practically all civil government matters.
James Madisons first act, after the First Congress was organized, in 1789, was to propose, on June 8, certain amendments, including what is now the First Amendment. His purpose was to “conciliate and to make all reasonable concessions to the doubting and distrustful”—to those, the Baptists, who were concerned about the issue of religious liberty. “Of all the denominations in Virginia, [the Baptists] were the only ones that had expressed any dissatisfaction with the Constitution on that point, or that had taken any action into looking to an amendment.” The Baptists of Virginia had also corresponded with Baptists of other states to “secure cooperation in the matter of obtaining” a religious liberty amendment. No other denomination asked for this change. A general committee of Baptist churches from Virginia presented an address to President Washington, dated August 8, 1789, expressing concern that “liberty of conscience was not sufficiently secured,” perhaps because “on account of the usage we received in Virginia, under the regal government, when mobs, bonds, fines and prisons, were [their] frequent repast.” President Washington assured them that he would not have signed the Constitution if he had had the slightest apprehension that it “might endanger the religious rights of any ecclesiastical society.”
Some Baptists and others did not see the need for a religious freedom amendment. Indeed, the First Amendment may not have been necessary to guarantee separation of church and state. Isaac Backus was elected as a delegate to the Massachusetts convention of January, 1788, which considered the issue of ratification of the new Constitution. He spoke at the convention.
“On February 4, [Backus] spoke of ‘the great advantage of having religious tests and hereditary nobility excluded from our government.’ These two items in the Constitution seemed to him a guarantee against any establishment of religion and against the formation of any aristocracy. ‘Some serious minds discover a concern lest, if all religious tests should be excluded, the congress would hereafter establish Popery, or some other tyrannical way of worship. But it is most certain that no such way of worship can be established without any religious test.’ He said ‘Popery,’ but he probably feared, as many Baptists did, that some form of Calvinism of the Presbyterian or Consociational variety was more likely. His interpretation of this article helps to explain why the Baptists [of Massachusetts] made no effort to fight for an amendment on freedom of religion along with the others which the convention sent to Congress.”
Even Madison, who proposed and fought for the First Amendment, did not believe that it was necessary for the security of religion. He wrote in his Journal on June 12, 1788:
“… Is a bill of rights a security for Religion? … If there were a majority of one sect, a bill of rights would be a poor protection for liberty. Happily for the states, they enjoy the utmost freedom of religion. This freedom arises from that multiplicity of sects, which pervades America, and which is the best and only security for religious liberty in any society. For where there is such a variety of sects, there cannot be a majority of any one to oppress and persecute the rest. Fortunately for this commonwealth, a majority of the people are decidedly against any exclusive establishment—I believe it to be so in the other states…. But the United States abounds in such a variety of sects, that it is a strong security against religious persecution, and it is sufficient to authorize a conclusion, that no one sect will ever be able to outnumber or depress the rest.”
Others were against a bill of rights. “James Wilson argued that ‘all is reserved in a general government which is not given,’ and that since the power to legislate on religion or speech or press was not given to the Federal government, the government did not possess it, and there was therefore no need for an express prohibition.” “Alexander Hamilton argued that a bill of rights, not only was unnecessary, but would be dangerous, since it might create the inference that a power to deal with the reserved subject was in fact conferred.”
The amendment was adopted on September 25, 1789, and was approved by the required number of states in 1791.
“No more fitting conclusion can be had … than to quote the language of the Father of his country. The days of persecution, of blood and of martyrdom were passed. Civil and soul liberty, the inalienable rights of man, enlargement, benevolent operations, educational advantages, and worldwide missionary endeavor, all had been made possible by the struggles of the past. The Baptists consulted George Washington to assist in the securing freedom of conscience. He replied:
“I have often expressed my sentiments, that every man, conducting himself as a good citizen, and being accountable to God alone for his religious opinions, ought to be protected in worshipping the Deity according to the dictates of his own conscience. While I recognize with satisfaction, that the religious society of which you are members have been, throughout America, uniformly and almost unanimously the firm friends to civil liberty, and the persevering promoters of our glorious revolution, I cannot hesitate to believe, faithful supporters of a free, yet efficient general government. Under this pleasing expectation, I rejoice to assure them, that they may rely on my best wishes and endeavors to advance their prosperity.”
 Charles F. James, Documentary History of the Struggle for Religious Liberty in Virginia (Harrisonburg, VA.: Sprinkle Publications, 2007; First Published Lynchburg, VA.: J. P. Bell Company, 1900), p. 167.
 Isaac Backus, A History of New England With Particular Reference to the Denomination of Christians called Baptists, Volume 2 (Eugene, Oregon: Wipf & Stock Publishers, Previously published by Backus Historical Society, 1871), p. 340.
Attempts to gain religious freedom continued. The Warren Association sent Isaac Backus to the Continental Congress in 1774 where he met with an Association of other Baptist churches from several adjacent colonies which had elected a large committee to assist. They presented their appeal for religious liberty. John Adams and Samuel Adams, neither of whom was a friend to separation of church and state, falsely asserted that Massachusetts had only a “very slender” establishment, hardly to be called an establishment, that the General Court was clear of blame and always there to hear complaints and grant reasonable help. While Mr. Backus was gone, the lie was spread that he had gone to Philadelphia to break the union of the colonies.
All the time these happenings were going on, the issues were being debated in the newspapers. The Warren Association continued to publish to the public instances of persecution as well as to actively seek religious liberty from the government. The Warren Association presented a memorial on July 19, 1775, requesting religious liberty and pointing out the inconsistency of rebelling against England for taxing without representation while doing the same thing in the colonies. Ultimately, nothing came of this. In 1777, Mr. Backus prepared an address, which was supported by a large number from various denominations, urging religious liberty to the Assembly which had been empowered to frame a new Constitution which was accomplished in 1780. The Third Article of the new constitution “excluded all subordination of one religious sect to another,” but imprisonment, and confiscation of property from men who refused to acknowledge such subordination continued.
In 1778, Mr. Backus wrote “Government and Liberty Described and Ecclesiastical Tyranny Exposed.” He quoted Charles Chauncy:
“We are in principle against all civil establishments in religion. It does not appear to us that God has entrusted the State with a right to make religious establishments…. We claim no right to desire the interposition of the State to establish that mode of worship, [church] government, or discipline we apprehend is most agreeable to the mind of Christ. We desire no other liberty than to be left unrestrained in the exercise of our principles in so far as we are good members of society.” This, said Backus, was all that Baptists asked. 
“Perhaps as a result of this tract, the General Assembly tried to conciliate the Baptists by appointing a Baptist minister to deliver the election sermon in May 1779. That minister, in his sermon, remained faithful to the principle of separation.”
Massachusetts began efforts to adopt a new constitution in 1777. The proposed constitution was defeated, but a new effort which began in 1779 proved successful. John Adams worked against the Baptist position at the convention. Mr. Backus, although not a delegate, went to Boston to stand for Baptist principles during the constitutional convention. He lobbied, wrote newspaper articles, published new tracts, and informed his brethren of what was going on.
Mr. Backus worked at the convention for a Bill of Rights. The first basic rights he listed were:
“All men are born equally free and independent, and have certain natural, inherent and unalienable rights, among which are the enjoying and defending life and liberty, acquiring, possessing, and protecting property, and persuing and obtaining happiness and safety.”
“As God is the only worthy object of all religious worship, and nothing can be true religion but a voluntary obedience unto his revealed will, of which each rational soul has an equal right to judge for itself; every person has an unalienable right to act in all religious affairs according to the full persuasion of his own mind, where others are not injured thereby. And civil rulers are so far from having any right to empower any person or persons to judge for others in such affairs, and to enforce their judgments with the sword, that their power ought to be exerted to protect all persons and societies, within their jurisdiction, from being injured or interrupted in the free enjoyment of his right, under any pretence whatsoever.”
Backus’ position, although seeking the same end, was from a different point of view than that of George Mason, Thomas Jefferson and James Madison.
“Three years earlier George Mason, with Jefferson’s approval and Madison’s amendments, had written a statement on religious freedom into the Bill of Rights in the Virginia Constitution:
‘That religion, or the duty which we owe to our Creator, and the manner of discharging it, can be directed only by reason and conviction, not by force or violence and therefore all men are equally entitled to the free exercise of religion, according to the dictates of conscience; and that it is the mutual duty of all to practice Christian forbearance, love, and charity towards each other.’
“Backus’s tone was that of a New Light pietist; Mason’s that of an Enlightened latitudinarian. The Virginians spoke of the ‘Creator,’ Backus spoke of ‘God.’ Mason stressed reason and duty, Backus stressed ‘religious worship.’ Backus referred directly to God’s ‘revealed will’ and to the ‘soul.’ Mason omitted any reference to them.
“The difference was obvious and fundamental. The Virginia separationists were interested in leaving the mind free to follow its own rational direction. The Massachusetts pietists believed that separation was necessary in order to leave the ‘rational soul’ free to find ‘true religion’ as expressed in the Bible, ‘the revealed will’ of God. Implicit in both statements was a belief in God, in natural law, in man’s ability to find them. But the deistic separationists of Virginia trusted entirely to man’s reason and free will. The pietists insisted that only through the supernatural grace of God would men find the Truth that is in Jesus Christ. Though both views were individualistic, the deist was anthropocentric, the pietist theocentric.”
The humanistic view of Mason, Jefferson, and Madison that man, through his reason could successfully address all his problems, and the humanistic goal of the “happiness of man” were inherent in the Declaration of Independence and the Constitution, the two greatest governing documents of all time, although blended with Biblical principles. Neither the name of Jesus nor the goal of “the glory of God” was in the Declaration of Independence or the Constitution.
The Warren Association, on September 13, 1780, published a remonstrance, authored by Mr. Backus, against Article Three of the proposed constitution. The remonstrance stated, among other things, that the provision therein requiring the majority of each parish “the exclusive right of covenanting for the rest with religious teachers,” thereby granting a power no man has a right to; and further stating that “the Legislature, by this Article, are empowered to compel both civil and religious societies to make what they shall judge to be suitable provision for religious teachers in all cases where such provision shall not be made voluntarily.” However, support for ministry could only be through voluntary support, not coercion that denied freedom of conscience. Backus and other Baptists “did not object to the view that Massachusetts should remain a Christian commonwealth; piety, religion, and morality could only be maintained with the institution of the public worship of God and of public instructions in piety, religion, and morality” were “generally diffused throughout the community.
“Jefferson, Mason, and Madison, designing the creation of a secular state, not only opposed all such practices but also objected to the use of chaplains in the Congress and armed forces, the authorization by the state of certain days of fasting, thanksgiving, and prayer; and the compulsory religious services in state universities. Jefferson explicitly stated that America was not and ought not to be a Christian country…. Backus never qualified his belief in a Christian commonwealth. He consistently argued for ‘a sweet harmony between’ Church and State. ‘It is readily granted,’ he wrote in 1784, ‘that piety, religion, and morality are essentially necessary for the good order of civil society.’”
 Isaac Backus, A History of New England With Particular Reference to the Denomination of Christians called Baptists, Volume 2 (Eugene, Oregon: Wipf & Stock Publishers, Previously published by Backus Historical Society, 1871), pp. 200-202, and fn. 1, p. 201.
 William G. McLoughlin, Isaac Backus and the American Piestic Tradition (Boston: Little, Brown and Company, 1967), p. 140. The entire tract is reproduced in Isaac Backus on Church, State, and Calvinism, Pamphlets, 1754-1789, Edited by William G. McLoughlin (Cambridge, Massachusetts: The Belknap Press of Harvard University Press, 1968), pp. 345-365.
 Again, the Constitution is the greatest governing document ever conceived by a nation, but the Biblical principle of “leaven”—bad doctrine always corrupts the good—has proven again, by the national experience, to be true. To understand and address a problem, one must be willing to face all the facts head on.
 Backus, A History of New England…, Volume 2, fn. 2, pp. 229-230.
 McLoughlin,Isaac Backus and the American Piestic Tradition, pp. 148-149.
At first the Separatists and Baptists desired to meet together. This proved untenable.
“[They] were bound together by the closest ties. The [Baptists] left the [Separate Congregational churches] with no ill feeling but with heartiest love, and this love continued, on both sides, after their separation. Their members had been converted together in the Great Awakening; together they had come out from the Standing Order; together they had suffered and were still suffering for the truth; they had the same enemies and oppressors; they felt the force of the same unjust and cruel laws; their plundered goods were sold at the same auctions, and their bodies confined in the same prisons; they had many kindred views and feelings, by which they sympathized most closely, and in which there were no others to sympathize with them. Moreover, they mutually desired inter-communion. Council after council and conference after conference recommended it, and there seemed to be no voice against it. And yet it failed. Practical difficulties arose…. The truth could not be escaped that Baptist churches, by renouncing infant baptism and sprinkling, and then practically recognizing them again as a proper declaration of discipleship and initiation to membership in the visible church, placed themselves in a position of direct inconsistency. One by one, reluctantly, but at last universally, they abandoned the untenable ground.—ED.”
By 1754, “the alliance between the two groups within Separatism was practically at an end, and the Baptist members left to form new churches or join existing ones.”
A Baptist church was instituted in Middleborough, Massachusetts by a number of brethren led by Mr. Backus from the Titicut Separatist church who were convinced communion should be limited to believers baptized upon a profession of their own faith. On July 23, 1756, Mr. Backus was installed as their pastor.
“He … published a discourse from Gal. iv. 31, to shew that Abraham’s first son that was circumcised was the son of the bond-woman, an emblem of the national church of the Jews; in distinction from regenerate souls, the spiritual seed of Abraham, of whom the Christian church was constituted; into which neither natural birth, nor the doings of others, can rightly bring any one soul, without its own consent. Upon these principles was the first Baptist church in Plymouth county then founded[.]”
 Isaac Backus, A History of New England With Particular Reference to the Denomination of Christians called Baptists, Volume 2 (Eugene, Oregon: Wipf & Stock Publishers, Previously published by Backus Historical Society, 1871), fn. 1, p. 115; on pp. 116-119 Backus gives further arguments.
 William L. Lumpkin, Baptist Foundations in the South (Eugene, Oregon: Wipf & Stock Publishers, 2006), p. 18.
Backus struggled with the issue of baptism, studied Scripture, rejected infant baptism, and was baptized by dipping on August 22, 1751. He set out to refute the anti-pedobaptist position by first turning to the Bible, and then to the claims of Baptist scholars in England that infant baptism was a corruption brought into the Christian church in the 2nd or 3rd century. What he found surprised him.
Next, Backus examined the Covenant Theology which lay at the heart of New England Puritanism. The relevance of this theology to Backus was mainly its effect on the church-state issue:
First, “[T]he Jewish church was clearly a national church, a theocracy in which Moses and Aaron ruled together, and thus the Puritans were able to utilize the covenant theology to justify their ecclesiastical laws and their system of territorial parishes and religious taxes. Second, the covenant theology provided the Puritans with justifications for the Halfway Covenant, thus polluting the purity of the mystical body of Christ. And in the third place the covenant theology, by emphasizing that grace ran ‘through the loins of godly parents,’ that the baptized children of visible saints were somehow more likely than others to obtain salvation, thereby established a kind of hereditary spiritual aristocracy; it also undermined the sovereignty of God by implying that God was bound by this covenant to save certain persons rather than others. [Etc.]”
The Puritans supported the unity of the Abrahamic Covenant in Romans 11.17.
“Here, the apostle Paul spoke of the Christian covenant as being grafted on to the Jewish covenant as a branch is grafted on to an olive tree, from whence the Puritans ‘argued the right of professors now to baptize their children, because the Jews circumcised theirs.’ This Backus rejected as misinterpretation. ‘The Jews were broken off thro’ unbelief, and the Gentiles were grafted in, and stand only by faith.’ Faith was essential to baptism. What Puritans stressed as organic continuity, Backus and the Baptists stressed as a complete break.”
Backus concluded that the Separates must explicitly reject the Covenant Theology, the whole conception of the corporate Christian state, which the Puritans had so painstakingly constructed in the wilderness of New England. Backus decided against infant baptism and was baptized. “[H]e rejected the Covenant Theology of the Puritans by arguing as the Baptists had long done that the Bible contained two covenants, the old Covenant of Works made with the Jews, and the Covenant of Grace made with those who believe in Christ….” “[T]he Puritans had confused the gospel of grace with the doctrine of works and transformed the gospel church of visible saints into a national church with a birthright membership.” “Backus and the Baptists stressed the discontinuity, the antithetical nature of the two, the complete and distinct break between the past and the present dispensations. That Americans were ready to grasp this new outlook after 1740 and to pursue it to its logical conclusions marks the real break with the Old World, the medieval mind and the Puritan ethos….”
 Isaac Backus, A History of New England With Particular Reference to the Denomination of Christians called Baptists, Volume 2 (Eugene, Oregon: Wipf & Stock Publishers, Previously published by Backus Historical Society, 1871), pp. 108-111.
 William G. McLoughlin, Isaac Backus and the American Piestic Tradition (Boston: Little, Brown and Company, 1967), pp. 61-63.
The church and state were interwoven in New England. Into the eighteenth century, the Puritan tradition continued in greater strength in Connecticut than elsewhere. The state taxed all citizens to support religion. In 1708, the Connecticut legislature ordained the Saybrook Platform. Under it, county associations of ministers met frequently to deal with matters of common interest, regional bodies called consociations were to handle all kinds of ecclesiastical difficulties, and a general state association exercised a general superintendency over churches and ministers. Under the Saybrook Platform, the county associations approved, licensed, and ordained the ministers of the parishes. The state supported the actions of the county associations, and could deny the right of a minister to preach and collect his salary.
Various struggles arose. In 1742 and 1743, laws were passed forbidding itinerant preachers from preaching without permission of the parish minister with penalty of imprisonment, excluding settled ministers who preached in any other parish without consent of the parish minister from any benefit of the laws for their support, removing from Connecticut any minister from any other colony who preached in Connecticut, and giving the legislature authority to license dissenting churches which complied with the British Toleration Act of 1689. The Legislature disciplined members of the Council and General Assembly known to sympathize with the New Lights. “Unauthorized schools and colleges were forbidden and only university graduates were eligible for ministerial standing before the law.” The county associations began to act. The New Haven Consociation in 1742 expelled pastors of established churches for preaching to a group of Separates and Baptists against the wishes of the established minister. In Canterbury, Windham County the majority of the church, New Lights, voted for a certain man to be pastor, but the Old Lights who were the majority in the parish voted for another. By law, both the church and parish had to concur, but the Windham Consociation declared that the minority of Old Lights in the church were the true church and ordained their choice. In Plainfield, the Windham Consociation “reversed the position it had taken in Canterbury and sided with a minority of Old Lights in the church to choose an Old Light minister over the objection of the majority of New Lights in the parish.”
The inequities and the persecutions by the established church and civil government resulted in more and more defections to the New Light position. The civil government used repressive measures to compel the Separates to return to the fold. “Revivalistic ministers were shut out of meeting houses; members were moved from civic office and, when they refused to pay taxes for support of the regular ministry, imprisoned.” At first most Separates that left the state-churches seemed destined to become Baptists. However, great disagreement arose between those who still adhered to infant baptism and those who insisted upon believer’s baptism—baptism after a confession of faith only. Because of this disagreement, the Baptist members left the Separate churches and formed their own churches.
This Separate movement had enduring consequences. One writer appropriately noted:
“[T]he Separatist movement is not appreciated as it deserves. We have too nearly forgotten our obligations to those men who dared to break away from the corrupt and worldly churches of the Standing Order, though they were armed with all the power of the State, of which they were a part, and to establish other churches in which vital godliness was the condition of membership. It was a transition movement, it is true, and of necessity only temporary, but its results were enduring. Many of the Baptist churches in New England spring from it directly, and through them, indirectly, almost all the rest; and other evangelical churches are largely indebted to it for their vitality and efficiency.—ED.”
 William L. Lumpkin, Baptist Foundations in the South (Eugene, Oregon: Wipf & Stock Publishers, 2006), p. 11; Isaac Backus, A History of New England With Particular Reference to the Denomination of Christians called Baptists, Volume 1 (Eugene, Oregon: Wipf & Stock Publishers, Previously published by Backus Historical Society, 1871), pp. 472-474; Isaac Backus, A History of New England With Particular Reference to the Denomination of Christians called Baptists, Volume 2 (Eugene, Oregon: Wipf & Stock Publishers, Previously published by Backus Historical Society, 1871), p. 319.
 William G. McLoughlin, Isaac Backus and the American Piestic Tradition (Boston: Little, Brown and Company, 1967), p. 24.
Mr. Clarke remained in England until, on July 8, 1663, he secured a new charter from Charles II. “By this Charter all the powers of government were conferred on the Colony, the King not having reserved to himself the right of revising its proceedings.” This charter was in effect until the constitution, which was adopted in November 1842, became operative the first Tuesday of May 1843. In addition to other matters, the charter cleared up land disputes with Massachusetts and some of the other colonies, provided for the organization of the government, and provided for freedom of conscience. That charter stated, in part:
Inhabitants of Rhode Island “pursuing, with peaceable and loyal minds, their sober, serious, and religious intentions, of godly edifying themselves, and one another, in the holy Christian faith and worship, as they were persuaded … did … transport themselves out of this kingdom of England into America,” and did then “leave their desirable stations and habitations, and with excessive labor and travel, hazard and charge did transport themselves into the midst of Indian natives” … “whereby, as is hoped, there may, in time, by the blessing of God upon their endeavors be laid a sure foundation of happiness to all America: And whereas, in their humble address, they have freely declared, that it is much on their hearts (if they may be permitted) to hold forth a lively experiment, that a most flourishing civil state may stand and best be maintained, and that among our English subjects, with a full liberty in religious concernments; and that true piety rightly grounded upon gospel principles, will give the best and greatest security to sovereignty, and will lay in the hearts of men the strongest obligations to true loyalty: … and to secure them in the free exercise and enjoyment of all their civil and religious rights, appertaining to them, as our loving subjects; and to preserve unto them that liberty in true Christian faith and worship of God, … that no person within the said colony, at any time hereafter shall be any wise molested, punished, disquieted, or called in question, for any differences in opinion in matters of religion, and do not actually disturb the civil peace of our said colony.” [Emphasis mine.]
The charter granted:
“unprecedented liberties in religious concerns. Moreover representation for the people and the limit of power to public officials provided a basic check and balance to popular sovereignty. The Royal Charter of 1663 proved to be distinctive, installing safeguards in the election process through the governing body of the State Assembly, made up of a governor, deputy-governor, assistants, and representatives from each of the towns,” each elected by the people.
The most important Biblical principle of the government they founded was incorporated into the supreme law of the United States of America by the First Amendment to United States Constitution.
As to the effect of the Rhode Island government thus established, John Callender wrote in 1838:
“The civil State has flourished, as well as if secured by ever so many penal laws, and in inquisition to put them to execution. Our civil officers have been chosen out of every religious society, and the public peace has been as well preserved, and the public counsels as well conducted, as we could have expected, had we been assisted by ever so many religious tests.
“All profaneness and immorality are punished by the laws made to suppress them; and while these laws are well executed, speculative opinions or modes of worship can never disturb or injure the peace of a State that allows all its subjects an equal liberty of conscience. Indeed, it is not variety of opinions, or separation in worship, that makes disorders and confusions in government. It is the unjust, unnatural, and absurd attempt to force all to be of one opinion, or to feign and dissemble that they are; or the cruel and impious punishing those, who cannot change their opinions without light or reason, and will not dissemble against all reason and conscience. It is the wicked attempt to force men to worship God in a way they believe He hath neither commanded nor will accept; and the restraining them from worshipping Him in a method they think He has instituted and made necessary for them, and in which alone they can be sincere worshippers, and accepted of God; in which alone, they can find comfort and peace of conscience, and approve themselves before God; in which alone, they can be honest men and good Christians. Persecution will ever occasion confusion and disorder, or if every tongue is forced to confess, and every knee to bow to the power of the sword: this itself is the greatest of all disorders, and the worst of confusions in the Kingdom of Christ Jesus.
“[T]his Colony with some since formed on the same model, have proved that the terrible fears that barbarity would break in, where no particular forms of worship or discipline are established by the civil power, are really vain and groundless; and that Christianity can subsist without a national Church, or visible Head, and without being incorporated into the State. It subsisted for the first three hundred years; yea, in opposition and defiance to all the powers of hell and earth. And it is amazing to hear those who plead for penal laws, and the magistrate’s right and duty to govern the Church of Christ, to hear such persons call those early times the golden age of Christianity.”
Mr. Clarke, on his return to Rhode Island, was elected Deputy-Governor three successive years. “He continued the esteemed pastor of the first Baptist Church of Newport, till his death” on April 20, 1676. Of Mr. Clarke, Isaac Backus wrote: He “left as spotless a character as any man I know of.” “The testimony which Backus proceeds to give of the purity of [Mr. Clarke’s] character and to his good name, even among his enemies, has been fully corroborated by later writers.” “To no man, except Roger Williams, is Rhode Island more indebted than to him.”
“An eminent American historian justly observed:
“The annals of Rhode-Island, if written in the spirit of philosophy, would exhibit the forms of society under a peculiar aspect. Had the territory of the State corresponded to the importance and singularity of the principles of its early existence, the world would have been filled with wonder at the phenomena of its early history.”
An example of the manner in which Rhode Island honored the doctrine of freedom of conscience is the way they upheld the standard in regards to the Quakers. Other colonies persecuted the Quakers from 1656 until 1661. Massachusetts hanged four Quakers who returned to the colony after being banished. The Commissioners of the United Colonies threatened Rhode Island with cutting off all commerce or trade with them if Rhode Island did not likewise persecute the Quakers by enacting penal legislation against them. Rhode Island “refused, and pointed out that it had no law for punishing people because of their utterances ‘concerning the things and ways of God, as to salvation and to eternal condition.’” The Commissioners of Rhode Island notified John Clarke. As a result, King Charles II ordered, “neither capital nor corporal punishment should be inflicted on Quakers, but that offenders should be sent to England.” This decree of the King probably saved the lives of other dissenters.
Not all that was happening was for naught. Isaac Backus wrote, “It is readily granted that the sentiments of Mr. Williams and Mr. Clarke, about religious liberty, have had a great spread since that day, so that men of a contrary mind cannot carry their oppressive schemes so far now as they did then,” but they still had a ways to go to achieve religious liberty. It was not until 1838 that John Callender declared “[t]he principles of religious freedom, which they [of Rhode Island] clearly and consistently maintained, are now the rule of action adopted by all Christian sects.”
 John Callender, The Civil and Religious Affairs of the Colony of Rhode-Island (Providence: Knowles, Vose & Company, 1838), Appendix XXI, pp. 261-262.
 Isaac Backus, A History of New England With Particular Reference to the Denomination of Christians called Baptists, Volume 1 (Eugene, Oregon: Wipf & Stock Publishers, Previously published by Backus Historical Society, 1871), pp. 277-280.
 See Callender, Appendix No. XXI, pp. 241-262 for the complete charter; see also, James R. Beller, America in Crimson Red: The Baptist History of America (Arnold, Missouri: Prairie Fire Press, 2004), Appendix D, pp. 505-506.
 Louis Franklin Asher, John Clarke (1609-1676): Pioneer in American Medicine, Democratic Ideals, and Champion of Religious Liberty (Paris, Arkansas: The Baptist Standard Bearer, Inc.), pp. 78-79.
Churches under Christ Ministry of Charity Baptist Tabernacle of Amarillo, Texas. A Christian Lawyer explains how a church in America can remain under the Lord Jesus Christ and Him only. "And hath put all things under his feet, and gave him to be the head over all things to the church" (Ephesians 1.22).