Well, it is indeed troubling if Vulcans actually pray. That is not a logical thing to do. Another reason to dislike Voyager, I guess.
Of main Starfleet personnel I can remember, closest of having religious faith comes Worf, who seems to genuinely believe things about Klingon afterlife (which probably is shown to actually exist or something in some episode or another.) However, even he doesn't worship any gods.
Gods in Star Trek always prove to be super-aliens/computers/impostors etc, and the Starfleet folks treat them as such, often denouncing them. In 'Who Watches the Watches' Picard is horrified that the Mintakans would revert back to their old superstitious ways, having already evolved past that state. It is clear there that humanity has long ago abandoned any such silliness.