Like other anti-intellectual postmodernists, I see you reconstruct history to suit your biases. Good luck on your self-deception. May you live to regret it in time.
First, you can't deny all the nasty governmental religious stuff that went on prior to our founding, and it would be stupid to think the Framers didn't know of that.
Nothwithstanding the general progress made within the two last centuries in favour of this branch of liberty, & the full establishment of it, in some parts of our Country, there remains in others a strong bias towards the old error, that without some sort of alliance or coalition between Gov' & Religion neither can be duly supported: Such indeed is the tendency to such a coalition, and such its corrupting influence on both the parties, that the danger cannot be too carefully guarded agst.. And in a Gov' of opinion, like ours, the only effectual guard must be found in the soundness and stability of the general opinion on the subject. Every new & successful example therefore of a perfect separation between ecclesiastical and civil matters, is of importance. And I have no doubt that every new example, will succeed, as every past one has done, in shewing that religion & Gov will both exist in greater purity, the less they are mixed together
Madison believed that religion and government were mutually corrupting and needed to be separated. He didn't believe religion itself was bad, or that the people expressing their religions was bad, but he believed that it shouldn't be mixed with state matters, lest both institutions be damaged.