Thomas Paine was the only outright atheist that I know of. The rest were mainly members of the Episcopal church which was/is hardly fundamentalist by today's terminology. Yes, there were Founding Fathers such as Benjamin Rush who could be classified as fundamentalist but the more prominent Founding Fathers just weren't all that religious although many did attend church services.
Thomas Paine is pushed as an Atheist/Deist, largly because of his work The Age of Reason that embraced French Rationalism, But were you aware that in later years he had a profound change and wrote:
"I would give worlds, if I had them, if the Age of Reason had never been written. O Lord, Help, Stay with me! It is hell to be left alone."
When Thomas Paine Gave his last words he said:
I die in perfect composure and resignation to the will of my Creator, God."