The intent was clear when you take into account the times. The head of the Church of England was the king. They didn’t want the head of state being the head of the church as well.
Atheists are a lot like liberals. They see things in the constitution that aren’t actually there.
It wasn’t strictly the Church Of England that motivated the Establsihment Clause, it was all the interminable wars on the European Continent driven by a State Church as well, but point well taken otherwise.