Persecuted Christians down through the ages have stood for separation of church and state. They refused, even under penalty of torture, imprisonment, and/or death to submit the church and spiritual matters to the ungodly, to the established church/state. This was apparent under the Roman Empire at the time of Christ and after, and after the wedding of church and state in the early fourth century. Although they differed from the Church of England and others on some doctrines, “[t]he Puritans brought 2 principles with them from their native country, in which they did not differ from others; which are, that natural birth, and the doings of men, can bring children into the Covenant of Grace; and, that it is right to enforce & support their own sentiments about religion with the magistrate’s sword.”.
“The religion of Jesus has suffered more from the exercise of this pretended right [to make religious establishments] than from all other causes put together; and it is with me past all doubt, that it will never be restored to its primitive purity, simplicity and glory, until religious establishments are so brought down as to be no more.”
“But this people brought two other principles with them from their native country, in which they did not differ from others; which are, that natural birth, and the doings of men, can bring children into to the Covenant of Grace; and, that it is right to enforce and support their own sentiments about religion with the magistrate’s sword.”
The “grand difficulty they [the Puritans] had with Mr. Williams was, his denying the civil magistrate’s right to govern in ecclesiastical affairs.” Roger Williams correctly observed, concerning persecution of Christians by the Roman Caesars:
- “Scripture and all history tell us, that those Caesars were not only arrogant, without God, without Christ, &c.; but professed worshippers, or maintainers, of the Roman gods or devils; as also notorious for all sorts of wickedness; and lastly, cruel and bloody lions and tigers toward the Christians for many hundred years.
- “Hence I argue from the wisdom, love, and faithfulness of the Lord Jesus in his house, it was impossible that he should appoint such ignorant, such idolatrous, such wicked, and such cruel persons to be his chief officers and deputy lieutenants under himself to keep the worship of God, to guard his church, his wife. No wise and loving father was ever known to put his child, no not his beasts, dogs, or swine, but unto fitting keepers.
- “Men judge it matter of high complaint, that the records of parliament, the king’s children, the Tower of London, the great seal, should be committed to unworthy keepers! And can it be, without high blasphemy, conceived that the Lord Jesus should commit his sheep, his children, yea, his spouse, his thousand shields and bucklers in the tower of his church, and lastly, his great and glorious broad seals of baptism and his supper, to be preserved pure in their administrations—I say, that the Lord Jesus, who is wisdom and faithfulness itself, should deliver these to such keepers? …
- “[W]hen the Lord appointed the government of Israel after the rejection of Saul, to establish a covenant of succession in the type unto Christ, let it be minded what pattern and precedent it pleased the Lord to set for the after kings of Israel and Judah, in David, the man after his own heart.
- “But now the Lord Jesus being come himself, and having fulfilled the former types, and dissolved the national state of the church, and established a more spiritual way of worship all the world over, and appointed a spiritual government and governors, it is well known what the Roman Caesars were, under whom both Christ Jesus himself, and his servants after him, lived and suffered; so that if the Lord Jesus had appointed any such deputies—as we find not a title to that purpose, nor have a shadow of true reason so to think—he must, I say, in the very first institution, have pitched upon such persons for thesecustodies utriusque tabulae, keepers of both tables, as no man wise, or faithful or loving, would have chosen in any of the former instances, or cases of a more inferior nature…” (Roger Williams and Edward Bean Underhill, The Bloudy Tenent of Persecution for Cause of Conscience Discussed and Mr. Cotton’s Letter Examined and Answered (London: Printed for the Society, by J. Haddon, Castle Street, Finsbury, 1848), pp. 204-205).
- “Christ never delivered His sheep or children to these wolves, his wife and spouse to such adulterers, his precious jewels to such great thieves and robbers of the world, as the Roman emperors were. Paul never appealed to Caesar as judge appointed by Christ Jesus to give definitive sentence in any spiritual or church controversy; but against the civil violence and murder which the Jews intended against him, Paul justly appealed. For otherwise, if in a spiritual cause he should have appealed, he should have overthrown his own apostleship and power given him by Christ Jesus in spiritual things, above the highest kings or emperors of the world beside…” (, p. 209).
- “A civil magistrate may be a good subject, a good magistrate, in respect of civil or moral goodness, which thousands want; and where it is, it is commendable and beautiful, though godliness, which is infinitely more beautiful, be wanting, and which is only proper to the Christian state, the commonweal of Israel, the true church the holy nation, Ephes. ii.; 1 Pet. ii” (, p. 212).
Weapons used for spiritual warfare are not suitable for earthly warfare and vice versa. Roger Williams pointed out:
- “[T]o take a stronghold, men bring cannon, culverins, saker, bullets, powder, muskets, swords, pikes, &c., and these to this end are weapons effectual and proportionable.
- “On the other side, to batter down idolatry, false worship, heresy, schism, blindness, hardness, out of the soul and spirit, it is vain, improper, and unsuitable to bring those weapons which are used by persecutors, stocks, whips, prisons, swords, gibbets, stakes, &c., (where these seem to prevail with some cities or kingdoms, a stronger force sets up again, what a weaker pulled down); but against these spiritual strongholds in the souls of men, spiritual artillery and weapons are proper, which are mighty through God to subdue and bring under the very thought to obedience, or else to bind fast the soul with chains of darkness, and lock it up in the prison of unbelief and hardness to eternity.”
Roger Williams maintained that the civil power has five proper political means to attain its end:
- “First, the erecting and establishing what form of civil government may seem in wisdom most meet, according the general rules of the word, and state of the people…. The magistrate has power to publish and apply such civil laws in a state, as either are expressed in the word of God in Moses’s judicials—to wit, so far as they are of general and moral equity, and so binding all nations in all ages—to be deducted by way of general consequence and proportion from the word of God.
- “For in a free state no magistrate hath power over the bodies, goods, lands, liberties of a free people, but by their free consents. And because free men are not free lords of their own estates, but are only stewards unto God, therefore they may not give their free consents to any magistrate to dispose of their bodies, goods, lands, liberties, at large as themselves please, but as God, the sovereign Lord of all, alone. And because the word is a perfect rule, as well of righteousness as of holiness, it will be therefore necessary that neither the people give consent, nor that the magistrate take power to dispose of the bodies, goods, lands, liberties of the people, but according to the laws and rules of the word of God….
- “Secondly, the making, publishing, and establishing of wholesome civil laws, not only such as concern civil justice, but also the free passage of true religion: for outward civil peace ariseth and is maintained from them both, from the latter as well as from the former.
- “Civil peace cannot stand entire where religion is corrupted, 2 Chron. xv. 3, 5, 6; Judges viii. And yet such laws, though conversant about religion may still be counted civil laws; as on the contrary, an oath doth still remain religious, though conversant about civil matters.
- “Thirdly, election and appointment of civil officers to see execution of those laws.
- “Fourthly, civil punishments and rewards of transgressors and observers of these laws.
- “Fifthly, taking up arms against the enemies of civil peace.”
On the other hand, according to Mr. Williams,
- “the means whereby a church may and should attain her ends, are only ecclesiastical, which are chiefly five. “First, setting up that form of church government only of which Christ hath given them a pattern in his word.
- “Secondly, acknowledging and admitting of no lawgiver in the church but Christ, and the publishing of his laws.
- “Thirdly, electing and ordaining of such officers only as Christ hath appointed in his word.
- “Fourthly, to receive into their fellowship them that are approved, and inflicting spiritual censures against them that offend.
- “Fifthly, prayer and patience in suffering any evil from them that be without, who disturb their peace.
- “So that magistrates, as magistrates, have no power of setting up the form of church government, electing church officers, punishing with church censures; but to see the church doth her duty herein. And on the other side, the churches, as churches, have no power, though as members of the commonweal they may have power, of erecting or altering forms of civil government, electing of civil officers, inflicting civil punishments—no, not on persons excommunicated—as by deposing magistrates from their civil authority, or withdrawing the hearts of the people against them, to their laws, no more than to discharge wives, or children, or servants, from due obedience to their husbands, parents, or masters: or by taking up arms against their magistrates, though they persecute them for conscience; for though members of churches, who are public officers, also of the civil state, may suppress by force the violence of usurpers, as Jehoiada did Athaliah, yet this they do not as members of the church, but as officers of the civil state.”
Paul instructed the church at Corinth to deliver a church member who was guilty of fornication with his father’s wife “to Satan for the destruction of the flesh, that the spirit may be saved in the day of the Lord Jesus.” He goes on to tell them that “a little leaven leaveneth the whole lump” and that they are not to “company with fornicators” “or with the covetous, or extortioners, or with idolaters” “or a railer, or a drunkard, or an extortioner.” The Corinthian church did expel the man and he repented and was restored. As Roger Williams points out, “Where it is observable, that the same word used by Moses for putting a malefactor to death, in typical Israel, by sword, stoning, &c., Deut. xiii.5, is here used by Paul for the spiritual killing, or cutting off by excommunication, 1 Cor.  v.13, Put away that evil person, &c. ”
Titus was instructed by Paul: “A man that is an heretick after the first and second admonition reject[.]” Roger Williams’ insights into this verse are instructive:
- “[F]or an erroneous and blind conscience, (even in fundamental and weighty points) it is not lawful to persecute any, til after admonition once or twice[.]”
- “First then Titus, unto whom this epistle and these directions were written, and in him to all that succeed him in the like work of the gospel to the world’s end, was no minister of the civil state, armed with the majesty and terror of a material sword, who might for offenses against the civil state inflict punishments upon the bodies of men by imprisonments, whippings, fines, banishment, death. Titus was a minister of the gospel, or glad tidings, armed only with the spiritual sword of the word of God, and [with] such spiritual weapons as (yet) through God were mighty to the casting down of strongholds, yea, every high thought of the highest head and heart in the world, 2. Cor. x. 4.
- “Therefore, these first and second admonitions were not civil or corporal punishments on men’s persons or purses, which courts of men may lawfully inflict upon malefactors; but they were the reprehensions, convictions, exhortations, and persuasions of the word of the eternal God, charged home to the conscience in the name and presence of the Lord Jesus, in the midst of the church. Which being despised and not hearkened to, in the last place follows rejection; which is not a cutting off by heading, hanging, burning, &c., or an expelling of the country and coasts; neither [of] which (no, nor any lesser civil punishment) Titus, nor the church at Crete, had any power to exercise. But it was that dreadful cutting off from that visible head and body, Christ Jesus and his church; that purging out of the old leaven from the lump of the saints; the putting away of the evil and wicked person from the holy land and commonwealth of God’s Israel, 1 Cor. v. [6, 7.] Where it is observable, that the same word used by Moses for putting a malefactor to death, in typical Israel, by sword, stoning, &c.,, Deut. xiii. 5, is here used by Paul for the spiritual killing, or cutting off by excommunication, 1 Cor. v. 13, Put away that evil person, &c.
- “Now, I desire the answerer, and any, in the holy awe and fear of God, to consider that—
- “From whom the first and second admonition was to proceed, from them also was the rejecting or casting out to proceed, as before. But not from the civil magistrate, to whom Paul writes not this epistle, and who also is not bound once and twice the admonish, but may speedily punish, as he sees cause, the persons or purses of delinquents against his civil state; but from Titus, the minister or angel of the church, and from the church with him, were these first and second admonitions to proceed.
- “And therefore, at last also, this rejecting: which can be no other but a casting out, or excommunicating of him from their church society.
- “Indeed, this rejecting is no other than that avoiding which Paul writes of to the church of Christ at Rome, Rom. xvi. 17; which avoiding, however woefully perverted by some to prove persecution, belonged to the governors of Christ’s church and kingdom in Rome, and not to the Roman emperor, for him to rid and avoid the world of them by bloody and cruel persecution.”
The lost man, the man who has not been born again, is a fleshly man who walks in the flesh without the indwelling Spirit of God. He is subject only to the law. The believer, a member of a church, a part of the body, is a heavenly man, and a stranger and pilgrim on the earth who is told to be led of the Spirit. A saved man and a church who love the Lord and want to glorify Him and who study the Word of God and specifically the Bible Doctrine of the church will stand for God’s principles regarding the church to the death; at least, that was the case of those martyrs for the faith who joyfully suffered and died rather than betray their Lord.
 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. 34-35.
 Backus, Volume 2, p. 249.
 Backus, Volume 1, pp. 34-35.
 Backus, Volume 1, p. 53; Armitage, The History of the Baptists, Volume 2, pp. 627-640.
 Roger Williams and Edward Bean Underhill, The Bloudy Tenent of Persecution for Cause of Conscience Discussed and Mr. Cotton’s Letter Examined and Answered (London: Printed for the Society, by J. Haddon, Castle Street, Finsbury, 1848), pp. 119-120.
 Ibid., pp. 212-213. See pp. 219-223 concerning the power of the magistrate in making laws.
 Ibid., pp. 213-214.
 1 Co. 6.1-5.
 1 Co. 6.7-11.
 See 2 Co. 7.8-11.
 Williams and Underhill, p. 62.
 Titus 3.10.
 Williams and Underhill, p. 20.
 Ibid., pp. 61-63.