Founder of Beliefnet, Steven Waldman, has published a book, Founding Faith: Providence, Politics, and the Birth of Freedom in America, and has offered up what he calls "Liberal Fallacy No. 1" at TPMCafe, attempting to refute the claim that all the men most intimately involved with the founding of the American Republic were Deists.
On the one hand, this is a good reality check, because they weren't all anything. I would be hard pressed to call Jefferson a "Founding Father" at all; he wrote the Declaration of Independence, plagiarizing John Locke along the way, but was not a delegate to the Constitutional Convention in 1787. Some of the most important men involved - Governeur Morris, Richard Henry Lee, Alexander Hamilton - are not remembered today as well as others, and were devoutly religious (Morris bankrolled the Revolution with his personal fortune; Hamilton was a sycophant, annoying George Washington; Richard Henry Lee was the grandfather of Robert E. Lee). Of all the men in Philadelphia that hot late summer of 1787, James Madison and Ben Franklin came closest, although as Waldman notes, Franklin implored his colleagues in Philly to pray together.
Deism is a tricky thing, though, so on the other hand, I wouldn't argue that some weren't Deists. Some might have been, or called themselves such. Indeed, Deism as a type of religious affectation was rare, and its impact on religious life overblown by a later intellectual community that sought to downplay what it saw as the superstitious aspects of Christian faith.
I think a far more honest way to present the whole issue of the Founders and their religious belief is this: The Founders understood their religious beliefs as being irrelevant to the vital issue of the structure of the American Republic, and the role of religion in public life to be corrosive to the practice of the virtues necessary to the success of republican life. With the example of a century and a half of religious war in Europe behind them, they knew all too well the dangers inherent in granting official status to one or another system of belief. Catholics, Protestants, Anabaptists, and non-believers managed to work together quite well in Philadelphia because they understood the issues they faced were narrow, practical ones. They hoped their example would be used in the future. Yet, the fourteen states each had official religions supported by state taxes. These were phased out over time, but were certainly present in 1787.
I think it far better to ask the question of the relevance of the religious beliefs of men living at the height of the Enlightenment trust in the rational life for those of us living at the tail end of such a time of optimism. With the screams of the victims of the 20th century still echoing in our ears, one wonders how we could continue to demand adherence to any particular ideology - and I include religious belief here - as a necessary qualification for inclusion in our national polity. One's belief, or lack thereof, in any system of belief, or even a vague acceptance of one or another "god", is irrelevant, in the end, to the more pressing question of whether and how well a man or woman is qualified to act on the public's behalf dealing with issues of vital import.
This is not stripping religion from the public square; I have yet to accept this particular idea. Indeed, this is one of the more stupid ideas presented in the past decade or so. What it is doing is keeping the Founders in view, while remaining true to our contemporary situation in which religious belief, while certainly vital to millions, no longer has the public voice it once did, and is far more a social and cultural palliative than part of the CV for public figures.
As an example, just consider that Bob Dole, George McGovern, Bill and Hillary Clinton, and George W. Bush are all members of the United Methodist Church. Indeed, Dole and McGovern were in leadership positions in the church in which they shared membership with Hillary and Chelsea Clinton.
Whether or not Madison, Jefferson, Washington, Adams, Franklin, or the rest of them were Deists or not is not nearly as important to me as whether or not they set up a system of government which continues to function in the 21st century. Ours is a secular state, if still a nation soaked in religious imagery (although the imagery is less and less evocative for the majority of the population).