What is religion, if not conjecture about the origin of mankind (and by extension the universe) that people believe without evidence?
I don't think that religion is predicated on the answering of prayers, or in a Creator who takes a special interest in some particular human.
Also, I don't think that either of those go against simulation theory; what if you're a sim in some alien version of The Sims, and they're going around fuckin with your life, removing ladders from your pools, etc.
Some religions don't either, and ST doesn't preclude it.