The idea that Thomas Jefferson was a lifelong unbeliever cannot be substantiated with the facts. Later in life, because of the influence of Unitarianism, he did begin to privately question key Christian doctrines. But earlier in his life, even when he was president, he was active as a professing Christian. And he certainly did not believe in stripping the public square from any reference to God or from Christian influence. Here are some examples from the book by Mark Beliles and me on Jefferson’s faith. In short, Jefferson did not advocate what Richard John Neuhaus termed “the naked public square”—turning America into a secular wasteland.
Toward the end of 1809, Jefferson’s practice of federal financial assistance of a Catholic missionary to the Indians was evident in a letter from Rev. Gabriel Richard who asked Jefferson to inform President Madison of the money promised him from the government.126 Jefferson forwarded it to Madison saying: “The inclosed letter is from Father Richard, the Director of a school at Detroit.” Jefferson forwarded to Madison another letter from Rev. Richard two years later, saying: “…you will see exactly how far he had a right to expect the government would go in aid of his establishment.” Clearly this shows more of Jefferson’s idea that government may help religion in the federal territories, even if not in the states.
Another example was in Jefferson’s dealings with Rev. John Cunow of the Society of the United Brethren [i.e., Moravians] for propagating the Gospel among the Heathen. The federal government, with Jefferson’s approval, had been supporting their missions to the Indians. Rev. Cunow was introduced to Jefferson by George Logan in December 1808 and Cunow gave the president a letter. In regard to this Jefferson wrote to Logan saying: “Your favor of the 8th. by mr Cunow was duly recieved & I now return you the letter it covered. mr Cunow’s object was so perfectly within our own views that it was readily obtained, & I am in hopes he has left us with a more correct opinion of the dispositions of the administration than his fraternity [i.e. the Moravians] has generally manifested.”