Thomas Jefferson, one of the Founding Fathers of the United States of America, played a major role in the establishment of the U.S, especially in helping shape the founding philosophies. His writings and ideals inspired others of his generation; they still inspire us today. Thomas Jefferson like all of the Founding Fathers believed in God. The U.S. was founded on Judeo-Christian beliefs and principles - the government was secular but the people were not. Jefferson, like the other Founding Fathers, knew however that state-sponsored religion too often led to oppression and loss of individual freedoms. He also knew that the converse was true - not allowing the free exercise of religion would also be harmful.
In 1779, Thomas Jefferson wrote a document called the Virginia Statute for Religious Freedom. This document was, in Jefferson's eyes, one of his greatest accomplishments. It was codified into law in Virginia a few years later. This document is important today because many who subscribe to secularism and atheism are trying to remove all religion from public discourse. Many view religion as nothing more than an aberration of a deranged mind. The Founding Fathers felt strongly the opposite - Jefferson included. I'll include a few highlights from this important document.
"Whereas Almighty God hath created the mind free; that all attempts to influence it by temporal punishments or burthens, or by civil incapacitations, tend only to beget habits of hypocrisy and meanness, and are a departure from the plan of the Holy author of our religion, who being Lord both of body and mind, yet chose not to propagate it by coercions on either..."
"...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 [this is true of both religious and non-religious beliefs], and as such endeavouring to impose them on others, hath established and maintained false religions [these "religions" could be secular] over the greatest part of the world..."
"...our civil rights have no dependence on our religious opinions, any more than our opinions in physics or geometry; that therefore the proscribing any citizen as unworthy the public confidence by laying upon him an incapacity of being called to offices of trust and emolument, unless he profess or renounce this or that religious opinion, is depriving him injuriously of those privileges and advantages to which in common with his fellow-citizens he has a natural right..."
"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 opinion in matters of religion, and that the same shall in no wise diminish enlarge, or affect their civil capacities."
"The rights hereby asserted [religious liberties] are of the natural rights of mankind, and that if any act shall be hereafter passed to repeal the present, or to narrow its operation, such act shall be an infringement of natural right." (Source, all emphasis mine).
Thomas Jefferson stated that mankind was created by God with a free will. He argued for separation of church and state because state-sponsored religions usually suppress the free exercise of other religions. What many secularists ignore is that Jefferson, in supporting a separation of church from state, was not arguing against religion at all; to the contrary, he believed that religions are vital (even if he wasn't particularly fond of the specific religions of the day). He argued for religious liberties. The free exercise of religion should play a large role in politicians' lives if they are religious. If they are not, then they should not be forced to accept any religion. He also stated that religious beliefs should not be given greater weight in political matters than mathematics or science (this means that religious beliefs should also not be given less weight either). In the end, Jefferson stated that religious liberties are "natural rights of mankind" - they are part of our fundamental rights.