That specific article may be a thing, but they're taking it out of context.
At that point in history, the Catholic Church was dominating England, and the King forced everyone to practice Catholicism. The Founding Fathers wanted to create a place where anyone could be free to believe whatever they wanted. So they made an article saying that the Government can't make one Religion better than any others, or try to silence people. But with "Separation of Church and State" Atheists are just trying to make sure they don't have to hear about God in the outside world. It's like if there was a law that said the Congress can't make a law respecting a political view, or prohibiting the free exercise", and Liberals used it to say "You can't talk about Right Wing Opinions in Public!".