I’m pretty sure that the Founding Fathers were more concerned with the rise and dominance of a “state” religion, such as the Church of England, than individual religions or an individual’s choice of religion (which was to be protected).
The creation of the United States followed a period in history where wars of religion wreaked tremendous havoc (the Thirty Years War, for instance). Many of the Founders or their contemporaries (Edmund Burke or Thomas Paine, for example) were very suspicious of state religions, or religion in general. Many, like Jefferson, were also Deists and felt that God had better things to do than meddle in temporal affairs.
I do agree that the idea of separation of Church and State has transmogrified as of late into anything having to do with religion, faith or spirituality is automatically considered anathema and should be banned. The cultural elites on the Left do consider any mention of God, faith or spirituality to be the mark of an unthinking, credulous idiot and I find that tremendously offensive. While my faith and religion (Catholicism) is certainly open to justified criticism, it also boasts some of the greatest thinkers and theologians in history.
As well as some outstanding football and basketball programs.