The founding fathers wanted not only to establish freedom of religion. They also wanted to establish freedom from religious bigotry and theocratic imposition. They wanted to ensure that no religious sect or denomination could dominate or rule, and they also wanted to ensure that no specific religion could dominate or rule.
Thomas Jefferson said: "The clergy, by getting themselves established by law and ingrafted into the machine of government, have been a very formidable engine against the civil and religious rights of man." – Thomas Jefferson, 1800
Madison, Franklin, Paine, Adams and others agreed with Jefferson, and later so did Abraham Lincoln.
Jefferson said: "Believing with you that religion is a matter which lies solely between man and his God, that he owes account to none other for his faith or his worship, that the legislative powers of government reach actions only, and not opinions, I contemplate with sovereign reverence that act of the whole American people which declared that their legislature should 'make no law respecting an establishment of religion, or prohibiting the free exercise thereof,' thus building a wall of separation between church and State." – Thomas Jefferson, 1802
Jefferson’s views on that matter were shared by most of the founding fathers. And the historic truth flies in the face of certain leaders of the so-called "Christian Right" in America, who have been and still are making false claims about the intent of the founding fathers, and they have misled many people in their spiritually blind flocks. In fact, they have succeeded to the extent that during the 2008 presidential election campaigns, being a Christian became a litmus test for being the President of the United States of America, and that is in direct violation of the intent of the founding fathers!
Most of the founding fathers were pluralistic and democratic in their views on religion. As I said, they did their best to ensure that there was a separation of church and state so that no religion or religious sect was favored or had dominant influence.
The writings of Jefferson, Madison, Adams, Paine and Franklin were particularly adamant about that. Their writings also show they were very wary and disapproving of religious superstition, bigotry, intolerance, hypocrisy, aggression, imposition, and persecution. They were very critical of certain right-wing Christian leaders in that regard.
In fact, Jefferson wrote: "The returning good sense of our country threatens the clergy and they believe that any portion of power confided to me will be exerted in opposition to their schemes. And they believe rightly; for I have sworn upon the altar of God, eternal hostility against every form of tyranny over the mind of man. But this is all they have to fear from me, and enough too in their opinion, and this is the cause of their printing lying pamphlets against me. . ."
Jefferson incurred the wrath of self-important and self-righteous Christian preachers who were much like the leaders of the "Christian Right" today, because he did not hide his disdain for them. He dared to echo the feelings of many of his fellow educated men of faith, as when he wrote: "Whenever preachers, instead of a lesson in religion, put [their congregations] off with a discourse on the construction of government, or the characters or conduct of those administering it, it is a breach of contract."
Clearly, Jefferson felt that preachers should not use their pulpit as a partisan political soap box, especially when their personal beliefs and opinions were presented as divine truth. Jefferson stood up to their political grandstanding cloaked in religion, and he exposed their "tyrannical" aggression and imposition. And they hated him for it.
But, you should know that, like me, Jefferson was only against the "corruptions" of Christianity, and against the religious bigotry and hypocrisy of arrogant, self-important and self-righteous people who claimed to be Christian authorities. Like me, Jefferson loved the actual teachings of Jesus. In fact, Jefferson wrote that: "Of all the systems of morality, ancient or modern, which have come under my observation, none appear to me so pure as that of Jesus."
Jefferson even compiled a reformed version of the gospels to rescue the philosophy of Jesus and the "pure principles which he taught," from the "corruptions and artificial vestments" which were established as "instruments of riches and power" for church patriarchs. Like me, Jefferson concluded that Jesus never claimed to be God, and he regarded much of the New Testament as corrupted with "palpable interpolations and falsifications." In other words, Jefferson separated ethical and true teachings from the religious doctrine and dogma and other fictional supernatural elements that were intermixed in the gospels between the mid-first century and the fourth century when the Christian Bible was compiled and edited. Jefferson called his book "The Life and Morals of Jesus of Nazareth Extracted Textually from the Gospels." He didn’t publish it, because he regarded religious beliefs as a private matter. But now people know it as The Jefferson Bible (of Jesus).
James Madison felt the same way Jefferson did about organized religious bigots. In 1875 Madison wrote: "What influence, in fact, have ecclesiastical establishments had on society? In some instances they have been seen to erect a spiritual tyranny on the ruins of the civil authority; on many instances they have been seen upholding the thrones of political tyranny; in no instance have they been the guardians of the liberties of the people. Rulers who wish to subvert the public liberty may have found an established clergy convenient auxiliaries. A just government, instituted to secure and perpetuate it, needs them not."
Madison also wrote: "Strongly guarded as is the separation between Religion and Government in the Constitution of the United States, the danger of encroachment by [Christian] Ecclesiastical Bodies, may be illustrated by precedents already furnished in their short history."
Benjamin Franklin, a founding father and a genius, felt the same way. He became a Deist after educating himself and turning away from his rigid and oppressive puritanical Protestant Christian upbringing. He learned to appreciate Deism, which was popular among many educated men of faith at the time, because it is the belief in the existence of God on the evidence of reason and nature, with rejection of superstition. That is why George Washington, John Adams, Thomas Jefferson, James Madison, and James Monroe, the first five presidents of the United States, were Deists, and their religious perspective was more close to that of today’s Unitarian Universalists than any other.
To give you an example of how Franklin felt, in an essay on "Toleration" he stated: "If we look back into history for the character of the present sects in Christianity, we shall find few that have not in their turns been persecutors, and complainers of persecution. The primitive Christians thought persecution extremely wrong in the Pagans, but practiced it on one another. The first Protestants of the Church of England blamed persecution in the Romish church, but practiced it upon the Puritans. [The Puritans] found it wrong in the Bishops [of the Church of England], but fell into the same practice themselves in New England [in America]."