For the most part, Star Trek is a hard-science universe and encourages us to view religions in that context. DS9 and TNG, for example, it’s clear that humans are generally atheists. When Picard interfered with that proto-Vulcan culture, he wouldn’t play to their belief systems because he refused to lead them down a bronze-age religious path. DS9 shows it fairly well, the Bajorans see the wormhole aliens as the prophets, but even to people who have witnessed them firsthand they still wouldn’t call them prophets regularly.

Take Star Trek: The Final Frontier. Kirk never once accepted they were going to meet god, and as soon as he confronted “god” he begain his kirkian mind games. One streak we notice with all the Trek captains is that they are astute students of the humanities. Kirk too has a deep appreciation for history and literature. So when he’s talking about God he’s not speaking as though he’s some southern baptist. I imagine he has a deep respect for religions and has studied them somewhat, but at the end of the day he’s a walking science book.