Jefferson's conviction that church and state must be kept separate was founded on reason. The question of what is truth, he felt, must be submitted to the free marketplace of ideas; it could not be determined by the state and imposed by coercion. "It is error alone which needs the support of government," he declared. "Truth can stand by itself."
Jefferson drafted his Statue for Religious Freedom in 1779. The [Virginia House of Delegates] terminated the official support for the Anglican church in that year, but it was not yet ready for Jefferson's concept of the total freedom to believe or, equally controversial, the freedom not to believe. The statute, which Jefferson later regarded as one of the three supreme achievements of his life [the other two being the Declaration of Independence and the founding of the University of Virginia], was finally steered through the assembly by [James] Madison in 1786.
"...the impious presumption of legislators and rulers, civil as well as ecclesiastical, who being themselves but fallible and uninspired men, have assumed dominion over the faith of others, setting up their own opinions and modes of thinking as the only true and infallible, and as such endeavoring to impose them on others, hath established and maintained false religions over the greatest part of the world, and through all time;...that our civil rights have no dependence on our religious opinions, any more than our opinions in physics or geometry; " (from Jefferson's "Statue for Religious Freedom")
Jefferson played into the hands of his critics by openly befriending the English scientist and religious nonconformist Joseph Priestly, who landed in Philadelphia in the mid-1790s with the specific intent of founding a Unitarian Church in America. English Unitarians were the fruit of rationalist seed of the Enlightenment; their name was derived from their supposed rejection of the Christian Trinity. Priestley's work The Corruptions of Christianity (1782), which denied the Trinity, virgin birth, original sin, and the divine inspiration of Scripture, had deeply influenced Jefferson's thinking…. While [Jefferson] was in [Philadelphia in 1797] he attended a series of sermons that Priestly gave before his new Unitarian congregation. This, incidentally, was the only time on record that Jefferson contentedly and regularly attended church services.
Writing on September 23, 1800, Jefferson told [Dr. Benjamin] Rush that he believed that the "tribe of clergy" who were in arms against him were inspired by self-interest. He felt they wanted to impose on the country their own brand of religion and saw him as the chief barrier to such a move. Added Jefferson: "And they believe truly. For I have sworn upon the alter of god eternal hostility against every form of tyranny over the mind of man."
[Jefferson] was never a deeply religious man. [H]e treated [the Bible] as a work of history, rather than the word of God. He believed in a rational, benevolent God, but he had grave doubts about other aspects of Christian theology. He accepted the teachings of Jesus but rejected much of the writings of the Apostles of the New Testament, as well as the doctrines of the early Christian church.
"The Jefferson Bible" originated...in the winter of 1798-1799. Benjamin Rush, an evangelical Christian…believed that a successful republic had to be founded on Christianity. Jefferson could not agree. Although in his youth Jefferson had favored the pre-Christian moralists, such as Socrates, [in April 1803] he...felt that the ethics of Jesus, if separated from the corruptions and superstitions of the Christian churches, "would be the most perfect and sublime that has ever been taught by man." In spare time during the remainder of his presidency he worked on …the "Syllabus of an Estimate of the Merit of the Doctrines of Jesus, Compared with those of Others" [the premise of which] was that the teachings of Jesus had been corrupted by theologians and churches; thus it was necessary to find the pure texts. Jefferson took up a New Testament and cut from the four books of the Evangelists those verses that had the authentic stamp of Jesus' thinking, "as easily distinguished," he thought, "as diamonds in a dunghill." …Jefferson returned to the task in 1816. What he wanted was a Bible of primitive Christianity, free of the mysticism of the later Testaments (the Book of Revelations, for instance) and the priestly canons for the third and fourth centuries. The scissors-and-paste job took three years, apparently because of the difficulty of finding Greek and Latin translations. …[H]e entitled it "The Life and Morals of Jesus of Nazareth."…This work, together with the Syllabus, constituted "The Jefferson Bible."
Source: "Thomas Jefferson" by Norman K. Risjord -- Madison House - 1994
[Benjamin Franklin] was the person most responsible, of all the Founders, for instilling in the new nation the virtue that is central to its role in the world struggle: that of tolerance, specifically religious tolerance.
In a world that was then, as alas it still is now, bloodied by those who seek to impose theocracies, Franklin helped to create a new type of nation that could draw strength from its religious pluralism. This comfort with the concept of tolerance—which was based on an aversion to tyranny, a fealty to free expression, a willingness to compromise, the morality of respecting other individuals and even a bit of humor and humility—is what most distinguishes America and its like-minded allies in the messy struggles that confront a new century.
Source: Time Magazine - "Citizen Ben's Greatest Virtues" -- by Walter Isaacson - July 7, 2003
When [Jefferson] had finished a draft [of the Declaration of Independence, he] sent it to Franklin on the morning of Friday, June 21. …Franklin made only a few changes. The most important of his edits was small but resounding. He crossed out…the last three words of Jefferson's phrase "We hold these truths to be sacred and undeniable" and changed them to the words now enshrined in history: "We hold these truths to be self-evident."..By using the word "sacred," Jefferson had implied, intentionally or not, that the principle in question--the equality of men and their endowment by their creator with inalienable rights--was an assertion of religion. Franklin's edit turned it instead into an assertion of rationality.
Source: Time Magazine - "How They Chose These Words" -- by Walter Isaacson - July 7, 2003
[On Lincoln (while not technically a "founding father," still one of America's most inspiring leaders):]
In May 1865, the Republican editor Josiah Holland interviewed the President's {Lincoln's] law partner William Herndon at length. When the subject of religion came up, Herndon told him, "The less said, the better," doubting that the pious Holland would want the details of Lincoln's unorthodox history. How, for example, Lincoln had doubted the divinity of Christ and the infallibility of the Bible. "Oh, never mind, " Holland said. "I'll fix that" -- and his book made Lincoln a model Christian.
Source: "The True Lincoln" by Joshua Wolf Shenk - Time Magazine - 7/4/05
The US government is not a theocracy. The founding fathers made sure that it was founded on the principle of separation of church and state.
Roger Williams, who was banished from the Puritan theocracy of the Massachusetts Bay Colony and founded the first Baptist congregation in colonial America {. . . } is also credited as the first person to use the phrase “wall of separation,” in a 1644 response to the theocratic Puritan clergyman John Cotton. (There should be a “wall of separation between the garden of the church and the wilderness of the world,” he wrote.) Thomas Jefferson used the expression in a famous 1802 letter to a Baptist congregation in Danbury, Conn.
Source: "The White House Is Tearing Down the Wall Between Church and State" By Susan Jacoby - NY Times - July 5, 2018
Source: Time Magazine - 7/7/03