Contrary to the mythical anti-Christian, anti-clerical Thomas Jefferson, our third president had many positive relationships with various clergymen of different Christian denominations. He did not view the FEDERAL government at the national level (as opposed to at the STATE level) as having any right to do anything religious per se. That said, he didn’t believe in the separation of God and state—the way it’s often presented today.
Some of the evangelicals in Jefferson’s day were concerned about any type of establishment of religion on the part of the federal government. They wrote to Jefferson asking about the practice of NATIONAL days of fasting and prayer. When Jefferson was the governor of the STATE of Virginia, he had no problem declaring a statewide day of fasting and prayer. As president, he did not apply the same principle to the federal government.
A religious freedom ally in the Valley of Virginia, Archibald Stuart, wrote Jefferson on June 4, 1801, saying: “I expect in process of time to hear some censures on the administration from the clergy [mainly from the northeast] on the score of publick fast & days of thanksgiving—Would it be worth while to anticipate these Cavils by takeing some favorable opportunity to deny the authority of the Executive to direct such religious exercises?…” Jefferson had yet to indicate that he would not proclaim a fast day as president, but this supporter already expected Jefferson’s administration to refrain because of the federalism principle that Jefferson and the Democratic-Republicans had already articulated. As Governor of Virginia, Jefferson had no problem declaring a Day of Prayer, and this was acceptable to his supporters but some felt that as president, such a move would usurp authority belonging to the people and the states. Although Jefferson agreed, he knew the political dangers of not calling for days of prayer and thanksgiving, as he wrote to Attorney General Levi Lincoln on August 26: “…From the clergy I expect no mercy. They crucified their Savior who preached that their kingdom was not of this world, and all who practice on that precept must expect the extreme of their wrath. The laws of the present day withhold their hands from blood. But lies and slander still remain to them.”
Again, it is obvious from all of the favorable relations with about 100 clergy that he had interacted with favorably up to this point that these comments of Jefferson are limited to those clergy aligned with the Federalist Party from New England (some of whom were Unitarians) and New York and none in Virginia and Washington.