There is currently a discussion taking place on the NRO's Corner concerning the Founding Father's religious beliefs and opinions. It was sparked by the publication of George Will's review in the NYT of a book called Moral Minority by someone named Brooke Allen. The debate is centered on the professed deism of most of the Founding Fathers. (I should note that I myself am a Deist, and at least partly due to the deism of the FF)
While I do not believe in religion (just a creator), intellectually I can appreciate the role that organized religion has played in civilization. In fact I believe that civilization is not possible without religion. I believe that most men (and women) are brutish by nature, and need an external force to moderate their behavior. Religion provides both a carrot and a stick, along with a justification, that encourages civil behavior.
When we look at societies that have attempted to suppress or eliminate religion (revolutionary France and various communist countries) we see a reversion to a State of Nature. (ie a lack of civilization)
Jefferson , Washington, Madison and the rest were intelligent enough to know that civilization and public order required the presence of a moral code and authority external to the State and society. They had to repose the origins of our rights in a creator in order to preserve them from destruction at the hands of a future despot.
As the Supreme Court has seen fit to transfer these rights from the realm of a creator to the realm of politics and judicial review, we have seen these rights threatened.
So yes, the Founding Fathers were skeptical of religion, but I firmly believe they understood it's utility and necessity.