To play devil’s advocate (and I've already spoken about this)
Star Trek never actually talked about religion. It just lectured you about breaking the Prime Directive. Every time "religion" shows up it’s like, “
Oops, we beamed down to this bronze age planet and now these villagers think the Enterprise-D
is Jehova."
True, the Native Americans on VOY were magic, incense-store bullshit. Native Americans on TV are never like, “
Here’s a retro but kinda interesting belief system & social structure,” it’s always, “
The eagle has whispered..." and portals opening to other dimensions.
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Eh, it was a fad. VOY chasing non-specific pop culture trends, as
Trek often does.
The American Indian Movement was a popular cause du jour in lefty Hollywood for about 3 months in 1973. It was to the point were Marlon Brando famously hijacked the Oscar ceremony to boycott his award (for The Godfather) and instead had
some Indian chick give a speech about Hollywood racism or something.
Rodenberry fully bought in to this fad, and remained obsessed with the movement long after everyone else had moved on. This is evidenced by TMP, where you can see a several background enterprise crewmembers in full stereotypical head dresses and face paint.
The TNG production team seemed to have merged this general sentiment with the "Indians are way spiritual and tuned into the environment bro" noble savage ideals that replaced religion for a good chunk of lefties in the 90's. So while traditional religion is bad, smoke lodges and hallucinatory drugs are progressive and enlightened.
Hence the garbage TNG episode where the wise Indians chastise Picard because his ancestors were puttering around in France when Americans fenced the western tribes into reservations and fed them firewater. And he's somehow even more evil now for wanting to relocate them to prevent the Cardassians from wiping them out for good this time.
The best part of this is that major sections of the AIM was just plainly fraudulent. For example, that woman giving Brando's protest speech was really half white / half Mexican, with no tribal affiliation at all. On topic, Voyager's producers brought on the famous consultant
Jamake Highwater, a Cherokee, to help guide Chakotay's character development. Unfortunately for all involved, it turned out
Highwater's real name was actually Jackie Marks. He was not a Cherokee. He was not an Indian. He was a 100% full blooded Ashkenazi Jew who watched too many westerns in the 1950's.
Literally everything about Native spirituality in Voyager was fake, being based solely on the fetishization of Indians by white LA shitlibs. This makes the character of Chakotay somehow more racist than that TNG Season 1 episode on the planet of the Africans, where Tasha Yar has to knife-fight the big boss lady on a jungle gym to get her bicycle back.