Thomas Jefferson was supported by some Baptists and Anti-Federalists, and disfavored by Congregationalists, Federalists, and others who believed in a stronger relationship between church and state. Jefferson and the Baptists worked closely in Virginia to disestablish the Anglican Church and establish religious freedom for dissenters. Baptists supported Jefferson’s bid for president because of his commitment to “the rights of conscience.” (italics added) Just for the record, I do not believe Jefferson evidences true Christianity; additionally, I do not believe that the Baptists who supported him believed that being a Christian was essential for public office, nor do I.
At times, Jefferson’s separationist view is presented as absolute, but it was not. As president he refrained from public religious proclamations (although I do not think those violate the First Amendment), but he did make such proclamations as governor of Virginia. For example, as governor he gave a proclamation appointing a day of “publick and solemn thanksgiving and prayer” in November 1779.
Moreover, even as president, he was not reticent in his use of religious language, which oftentimes was virtually impossible to distinguish from prior religious proclamations. Following are samplings of such language.
In his first inaugural address…gratefully acknowledging “an overruling Providence,” Jefferson wrote: “And may that Infinite Power which rules the destinies of the universe, lead our councils to what is best, and give them a favorable issue for your peace and prosperity.” His first annual message to Congress brims with thanksgiving: “While we devoutly return thanks to the beneficent Being who has been pleased to breathe into them the spirit of conciliation and forgiveness, we are bound with peculiar gratitude to be thankful to him that our own peace has been preserved through so perilous a season, and ourselves permitted quietly to cultivate the earth and to practice and improve those arts which tend to increase our comforts.” His second annual message opened with the following thanksgiving: “When we assemble together, fellow citizens, to consider the state of our beloved country, our just attentions are first drawn to those pleasing circumstances which mark the goodness of that Being from whose favor they flow, and the large measure of thankfulness we owe for his bounty.” Jefferson concluded his second inaugural address by asking Americans to join with him in prayer that the “Being in whose hands we are…will so enlighten the minds of your servants, guide their councils, and prosper their measures, that whatsoever they do, shall result in your good, and shall secure to you the peace, friendship, and approbation of all nations.” His public papers are replete with expressions of thanksgiving and devotion….In marked contrast to the separationist message of the Danbury letter, Jefferson demonstrated a willingness to issue religious proclamations in colonial and state government settings. For example, as a member of the House of Burgesses, on May 24, 1774, he participated in drafting and enacting a resolution designating a “Day of Fasting, Humiliation, and Prayer.” Jefferson recounted in his Autobiography: “We were under conviction of the necessity of arousing our people from the lethargy into which they had fallen, as to passing events [the Boston port bill]; and thought that the appointment of a day of general fasting and prayer would be most likely to call up and alarm their attention….[W]e cooked up a resolution…for appointing the 1st day of June, on which the portbill was to commence, for a day of fasting, humiliation, and prayer to implore Heaven to avert from us the evils of civil war, to inspire us with firmness in support of our rights, and to run the hearts of the King and Parliament to moderation and justice.” ….In 1779, when Jefferson was governor of Virginia, he issued a proclamation appointing a “day of publick and solemn thanksgiving and prayer to Almighty God.” (This proclamation was issued after Jefferson had penned his famous “Bill for Establishing Religious Freedom.” Also, in the late 1770s, as chair of the Virginia Committee of Revisors, he was chief architect of a revised code that included a measure entitled, “A Bill for Appointing Days of Public Fasting and Thanksgiving.”…The bill authorized “the Governor, or Chief Magistrate [of the Commonwealth], with the advice of the Council,” to designate days for thanksgiving and fasting and to notify the public by proclamation…. “Every minister of the gospel shall on each day so to be appointed, attend and perform divine service and preach a sermon, or discourse, suited to the occasion, in his church, on pain of forfeiting fifty pounds for every failure, not having a reasonable excuse.” Although the measure was never enacted, it was sponsored by Madison….The final disposition of this legislation is unimportant to the present discussion. The relevant consideration here is that Jefferson and Madison jointly sponsored a bill that authorized Virginia’s chief executive to designate days in the public calendar for fasting and thanksgiving.
In light of these events, and that Jefferson did not draft the First Amendment, the phrase “wall of separation” should not be the gloss or final word on the First Amendment. He was minister to France and was out of the country when the Bill of Rights was adopted. He neither participated in the Constitutional Convention nor the First Federal Congress that in the summer of 1789 debated the content of a provision, which came to be known as the First Amendment that was later approved in September. In addition, “it is obviously incorrect to substitute this private opinion for the First Amendment.”
Therefore, the phrase “wall of separation,” along with the First Amendment, actually has for its purpose providing for the freedom of religion not freedom from religion. Therefore, in light of Jefferson’s practice as governor, communication with the Baptists, and his second inaugural address as president, it seems clear that he emphasized a jurisdictional understanding of the First Amendment based on federalism and freedom of conscience. Thus, in light of Jefferson’s statements and behavior, the theist is free to follow God both privately and publicly, and the atheist is equally free not to do so.
 Herbert M. Morais, “Life and Words of Elder John Leland” (M.A. thesis, Columbia University, 1928), 44-50 as quoted by Daniel L. Dreisbach, Thomas Jefferson and the Wall of Separation between Church and State, (New York: New York University Press, 2002), 13.
 Dreisbach, Thomas Jefferson, 137, Appendix 4.
 Selected texts from Dreisbach, Thomas Jefferson, 57-59
 Ibid., 98.
 Joseph H. Brady, Confusion Twice Confounded: The First Amendment and the Supreme Court: An Historical Study (South Orange, N.J.: Seton Hall University Press, 1954), 74, as quoted by Dreisbach, Thomas Jefferson, 224.