Forgot about that, but still, he isn’t from Earth. He learned from his grandfather on a planet given to Native Americans (a great big reservation?)
True he was from a Federation Colony established by people from Earth, but his tribe still had ties to Earth. I believe there was an episode where he and his father went on a quest to meet fellow descendants of the Rubber Tree People who worshiped the “Sky Spirits”. So their religion did have a component that was shown to still exist on Earth in universe in 2344 as I recall.
Speaking of religion in Trek, I just remembered that there were at least two other instances of religion playing into Voyager. Neelix’s beliefs were explored quite vividly in the episode where he was actually dead for 17 hours before being brought back by Borg ingenuity. And Janeway’s beliefs were somewhat touched on in the episode Coda. Though her belief was more that she didn’t have any belief but science in life but didn’t discount the idea of an afterlife.
There was also Earth religions in TOS quite a few times. The most obvious being in my favorite episode “Balance of Terror”, where there’s a wedding at the beginning in the ship’s chapel. The chapel contained religious symbols from many religions including a cross. And indeed the newly married widow at the end prays in the chapel at the end of the episode. Other instances included a clearly Hindi crewmember with a Bindi in “That Which Survives.” And I believe Psalm 95 is referenced in “The Empath”. And the episode “Bread and Circuses” actually mentions the Son of God while the crew are on a parallel developed Earth where Rome still existed at a 20th century level of development.
TNG had a few references to human Religion… Data references Hinduism in at least one episode indicated it survives in universe to the 24th century. And one episode “Sub Rosa” showed a church with cemetery on a Federation Colony. During the funeral in that episode you can even hear the funeral attendees say “Amen” at one point.
DS9, in addition to the Bajoran religion which was central to the show, Capt Sisko’s dad actually quotes from the Bible in “Far Beyond the Stars”. And his fiance Cassidy actually says she’s like a priest to perform their wedding (and she’s not referencing Bajoran priests in this instance).
Enterprise probably had the most obvious references to human religion however. Dr. Phlox mentions he had studied at a Tibetan monastery and that he’d attended mass in St. Peter’s Square. Which means that the Vatican survives in universe until at least the 2150’s.
So it seems that into the Star Trek era that Christianity, Hinduism, Buddhism, and Native American Religions all survive in some form.