A majority were. A notable many were not. My fifth-great-uncle was certainly among those who were. It is quite fine that many were not. We have many today who are not exactly religious, but are good men. We also have a majority who are religious, and many who are at least good men. This is nothing to be so anxious about. I understand that many want to be the same as the "Founding Fathers", and you in some way, want them to be similar to you, but it isn't necessarily so.
Glenn Beck and his "followers" (I would be more apt to say "spirited comrades") may claim to be on the side of the "Founding Fathers", but part of it is pure fantasy. The point is, most of our "Founding Fathers" were Christian, but many who were more famous than others, were also Deist. And it is quite alright to stop short of "their" beliefs, because to a degree, we can't join them. At any rate, due to the nature of a majority being Christian, their "Christian" attitudes and quirks become apart of the nation, perhaps more so than they could have figured out. It doesn't mean that they didn't perceive a difference between government and religious organization, but it could mean that some had different perceptions of what that difference entailed. This also explains why those like Jefferson were so unique in how far they wished to create the divide between state and religion (Virginia and University of Virginia), whereas others were not so predisposed.