Of all American presidents, Thomas Jefferson most strongly maintained the ideals of religious freedom and the separation of church and state.
In religious terms, Thomas Jefferson was perhaps the most radical president in American history. He supported religious freedom for all. His personal beliefs were based on reason rather than faith. And he insisted on maintaining a strict separation between government and religion.
Freedom of – and From – Religion
Early in his political career, Jefferson set forth his belief that governments had no legitimate authority in matters of religion. In his Notes on the State of Virginia (1785) he wrote: “The legitimate powers of government extend to such acts only as are injurious to others. But it does me no injury for my neighbor to say there are twenty gods or no god. It neither picks my pocket nor breaks my leg.”  Even earlier, in 1777, he had drafted a bill to establish religious freedom in Virginia. The key paragraph stated: “We the General Assembly of Virginia do enact that no man shall be compelled to frequent or support any religious worship, place, or ministry whatsoever, nor shall be enforced, restrained, molested, or burdened in his body or goods, nor shall otherwise suffer, on account of his religious opinions or belief; but that all men shall be free to profess, and by argument to maintain, their opinions in matters of religion, and that the same shall in no wise diminish, enlarge, or affect their civil capacities.” 
A Religion of Reason
Jefferson admired the ethics of Jesus, calling his system of morality “the most benevolent & sublime probably that has been ever taught….” But regarding the divinity of Jesus, Jefferson dismissed the idea as “foreign to the present view,” which was limited to matters of his ethical teachings only.  Jefferson was also alarmed at the growth of what he called “fanaticism” in religion, writing late in his life, “The atmosphere of our country is unquestionably charged with a threatening cloud of fanaticism, lighter in some parts, denser in others, but too heavy in all….” Ever the optimist, he saw more widespread education as the antidote to unreasoning faith: “The diffusion of instruction, to which there is now so growing an attention, will be the remote remedy to this fever of fanaticism….” 
The Wall of Separation
During his second term as president, Jefferson was asked by the clergy of several churches to proclaim a day of prayer and fasting. He declined to do so, nor would he even recommend to the states that they proclaim such an observance. He wrote to one of the ministers: “Fasting & prayer are religious exercises…. Every religious society has a right to determine for itself the times for these exercises, & the objects proper for them, according to their own particular tenets; and this right can never be safer than in their own hands, where the constitution has deposited it…. Be this as it may, everyone must act according to the dictates of his own reason, & mine tells me that civil powers alone have been given to the President of the U.S. and no authority to direct the religious exercises of his constituents.” 
Throughout his public and private life, Thomas Jefferson believed that religion should be based on reason; that all people have a right to choose their own religion, or none; that behavior is more important than belief; and that religion and government should never be intertwined. Few, if any, of his successors have held as strongly to these principles.
-  Peterson, Merrill D., Ed. Thomas Jefferson: Writings. New York: The Library of America, 1984, p. 285.
-  Ibid., p. 347.
-  Ibid., p. 1121.
-  Ibid., pp. 1463-4.
-  Ibid., p.1187.