What I know of the founding fathers' religious beliefs is that they were mostly deists. They believed that there was some form of god that created the universe (which was hard to not believe at the time), but they didn't believe it was a personal god that cared about us in any important way. Most felt organized religion was merely a tool to control the masses, and played the part of the devout Christian in public.
Check out Thomas Jefferson's The Life and Morals of Jesus of Nazareth (aka the Jefferson Bible) or Thomas Paine's The Age of Reason.
One could probably argue that men like Jefferson were strongly influenced by their Christian backgrounds, but I would argue that a larger cultural evolution that gradually lead to the widespread adoption of Christianity amongst Europeans is what also lead to men like Jefferson ridding themselves of organized religion and coming to hold the values they did.
