Contrary to the mythical Thomas Jefferson, the real Jefferson was a professing Christian (who later in life had some serious, private doubts). He had many good relationships with many Christian leaders. He said that Jesus (“the holy author of our religion”) is the reason we should have religious freedom. That is because Jesus gave us freedom to accept Him or reject Him. It is not up to the state to determine what religion people should practice (if any). Jefferson believed in the separation of the institution of the church from the institution of the state. He did not believe in the separation of God and government. Here is a portion of our book, DOUBTING THOMAS, where in the early 1820s, Jefferson began to have some conflicts with some Presbyterians over some specifics at the non-sectarian college he was establishing (the University of Virginia).
Presbyterian Rev. Conrad Speece passed through and preached in the Charlottesville courthouse in 1818 and felt the city was under Satan’s control, and that’s why he advocated for the new university to be established there. Rev. Benjamin Holt Rice settled in as the permanent pastor in 1822 with Rev. Francis Bowman as his assistant. Benjamin Rice also preached in the Episcopal church building near Keswick (unofficially known as Walker’s Church), since it had no regular minister, and was well-received even by some of Jefferson’s family members, such as Granddaughter Ellen Coolidge who attended Rice’s preaching and later wrote of how his messages moved her.87 So Presbyterian and Episcopalian churches were the first to get reestablished in the area.
To orthodox Christians who only heard of the Unitarian Cooper’s hiring and nothing of the failed attempt to get Rev. Knox, it appeared that the University of Virginia was going in the direction of Unitarianism as Harvard had recently done up north. It was then that Rev. John Holt Rice (brother of Benjamin Rice above), just weeks away from the vote in the legislature to charter the new university, began in his influential Evangelical Magazine to publicly call for the firing of Unitarian Thomas Cooper as a professor. If Presbyterians pulled their support the university would likely not succeed. Rice wrote on January 10, 1819: “A critical time in our state is approaching. Religion is to triumph before long or the pestilence of Socinianism [i.e., Unitarianism, will grow];…They fear a defeat [in the legislature], and dread Presbyterians most of all. I have…[however] gone in among the Monticello-men, and assured them that…far from being opposed, we are ready to give all our aid in the establishment, support, and proper management of such an institution.”
The charter passed but Jefferson truly did not understand the uproar among Presbyterians, as a form of Unitarianism had been acceptable among evangelicals (Restorationists) in the Piedmont for years. Although Jefferson knew the board was not favoring Unitarianism, he couldn’t see how it appeared to the evangelical public. So he began to attribute the criticism to a desire among Presbyterian clergymen to control the university for themselves. Jefferson was also embarrassed and angry at what he thought was a betrayal by Presbyterians who had supported the school so far. In the heat of the moment, Jefferson’s first private letters against Virginia Presbyterians were written the following year in 1820. The only other time Jefferson made any statement critical of Christian leaders in Virginia was one reference to the Episcopalians in 1785—thirty-five years earlier! Almost all other of his anti-clergy remarks were about northerners (“Easterners”) or Europeans. This criticism now of Virginia clergy by Jefferson was really unfounded and unfair, but thankfully his targets never knew of it since it was done in a few private letters.