My main point here is in talking about religion and our founding fathers one can't ignore the timeframe they were living in. The were experiencing the influence of Europe's Age of Enlightenment in which all in the past was being questioned. It was a time when the fundamental view of government was evolving. Superstition and religion were taking a back seat to science.
It was also a time when human rights were being advocated. During the time of the American Constitution at a national level it was problematic. But it did come about within the section of America as our nation's leaders set policies for opening the Northwest Territory, the land that later became the states of Ohio, Indiana, Michigan, Illinois and Wisconsin. In this land slavery was forbidden. As was any state religion. The policy also mandated that a section of each township was to be set aside to support public education.
Thomas Jefferson's Bill for Establishing Religious Freedom declared, "that our civil rights have no dependence on our religious opinions, any more than our opinions in physics or geometry."