Seriously though, what the founding fathers wanted is not so relevant 200 years later...
Whether or not any of them actually called for the separation of church and state, we need to recognize that the USA is much bigger and much more diverse in its races, cultures and belief systems than it was in the late 18th century. Science has also made gigantic leaps since then, and we've learned more about the politics and economics that generate a (relatively), stable middle-class. The obvious choice to fit in with all of these factors is secularism. It's not about right or wrong, who wanted what, or even religion all together. It's just pragmatism.