I love the Bajorans and their struggles, both externally and within their own politics and religion. I think most people who got bored with the Bajorans were just hoping for more battles against the Borg.

They might’ve even been turned off by the focus on religion in the first place. Roddenberry was famously outspoken against religion (due to rejecting his upbringing). I think TOS and TNG went pretty far towards cultivating a large audience of atheist and agnostic fans. Many of these would’ve been pretty turned off by the depiction of religious characters in anything but a negative light. When you go from being raised religious to being an atheist who rejects all that, it’s hard to walk back to being neutral or open-minded about religion once again.