I can’t speak for the OP, but…
Histocially, European colonialization crushed many religions with the expressed aim of replacing them with Christianity in one form or another. Also, non-Christian religions were a major rallying point for resistance to colonialization. So, when a Western TV show or Westerners in general says it’s time to “move past” religion, I can understand people seeing it as a continuation of five hundred years or so of attacks on non-Christian religions.
Of course, there are plenty of other examples of non-Christian inter-religious conflict in history and even in current events, but for people whose countries suffered under European colonialization, it’s not surprising they might see things through that lens primarily.
To bring this back to DS9, the Cardassians certainly suppressed the Bajoran religion during the Occupation, and we’ve seen the Bajoran faith was a meaningful part of the resistance for many, which is why it’s understandable that a lot of Bajorans might get bent out of shape when, say, a Federation teacher tells her students that the Prophets are just super-advanced aliens and that the Celestial Temple is an understandable astrophysical phenomenon. While it’s also understandable that said teacher might insist that teaching the scientific truth is the right thing to do, especially given she’s teaching in a Federation school.
So is the Federation guilty of cultural imperialism? Or are the Bajorans being xenophobic? Or can both be true?
All great fodder for drama.
At least that’s how I saw things when I wrote for DS9.