Congregational Churches Cleared; a treatise crammed, in the opinion of an admirer, with “most practical Soul-searching, Soul-saving, and Soul-solacing Divinitie,” “not Magisterially laid down, but friendly debated by Scripture, and argumentatively disputed out to the utmost inch of ground.” The partisan purpose of the book was to prove that Congregationalism, as practised in New England, was nearer akin to aristocratic Presbyterianism than to democratic Brownism; and of this purpose he speaks frankly:
Out of this same theocratic root sprang the well-known dispute with Roger Williams concerning toleration. Not freedom to follow the ways of sin, but freedom to follow the law of God-this was Cotton's restriction upon the “natural liberties” of the subject of Jehovah. There must be freedom of conscience if it be under no error, but not otherwise; for if freedom be permitted to all sinful errors, how shall the will of God prevail on earth? In this matter of toleration of conscience, it is clear enough today that the eyes of the great theocrat, “so piercing and heavenly (in other and precious Truths of God）” --as Roger Williams acknowledged — were for the moment sadly “over-clouded and bloud-shotten.” But for this the age rather than the man was to blame. It was no fault of John Cotton's that he was the product of a generation still resting under the shadow of absolutism, unable to comprehend the more democratic philosophy of the generation of Roger Williams. He reasoned according to his light; and if he was convinced that the light which shone to him was a divine torch, he proved himself thereby a sound Puritan if not a good Christian. The native sweetness and humanity of Cotton's character, despite his rigid theocratic principles, comes out pleasantly when the great preacher is set over against the caustic lawyerminister
Neither is it the Scope of my whole Book, to give the people a share in the Government of the Church. . . . Nay further, there be that blame the Book for the other Extreme, That it placeth the Government of the Church not at all in the hands of the People, but of the Presbyterie.Part II, p. 15.