Jefferson argued that the Lord's way is to allow humans to find their way to Him, not through revelation or blind faith but through reason: The "holy author of our religion, who being lord both of body and mind, yet chose not to propagate it by coercions on either, as was in his Almighty power to do, but to exalt it by its influence on reason alone. The legislature apparently believed Jefferson went too far with the emphasis on reason, deleting his contention that religion would "extend it by its influence on reason alone."
Jefferson declares that the alliance of sword and cross had promulgated "false religions over the greatest part of the world and through all time." The statute substituted a concept which today seems obviously in tune with our free market sensibility but was novel then: false religious ideas will lose as long as there is a free exchange of ideas. As Jefferson put in one of the most memorable lines in the statute, "truth is great and will prevail if left to herself."
Almighty God hath created the mind freeWhereas James Madison's Memorial and Remonstrance had defeated one particular plan for state-supported religion, the Statute for Religious Freedom attempted to make the principle permanent. "To compel a man to furnish contributions of money for the propagation of opinions which he disbelieves, is sinful and tyrannical."
Some religious conservatives have argued that the statute's reference to the "holy author of our religion" showed that even Jefferson was referring to Christianity. At first glance, they have a point. Surely it could not have been accidental that a pluralist like Jefferson chose to use the singular form of the words "author" and "religion." Jefferson himself cleared up the ambiguity in his autobiography. He reported that an amendment had been offered to change that phrase from "holy author of our religion" to "Jesus Christ" but that "the insertion was rejected by a great majority, in proof that they meant to comprehend, within the mantle of its protection, the Jew and the Gentile, the Christian and Mahometan, the Hindoo, and infidel of every denomination."