Just perused this thread, two things stand out:
Country stereotypes: If they took the image of country life which may well be completely different in the 24th century, it is possible that Paris' mind in particular or even Janeway's was idealized, generalized, and homogenized, with the result we saw on screen.
Indian stereotypes: Chakotay seems to be written as many real life individual Indians I've seen on TV who are making an effort
to preserve specific aspects of their past. As such I don't find fault with the character, even if I find fault with the beliefs themselves. I don't think we are menat to believe all Indians (Native Americans) subscribe to such beliefs. I think we're also led to believe this is an aspect of being different or even a rebel that manifests itself within Chakotay to the point he does something else others wouldn't: join the Maquis.
I'm not actually a huge fan of Robert Beltran's acting, but I recall seeing the producers made an effort not to be stereotypical. For the most part Chakotay did seem like a professional 24th century, former Starfleet member.