I think the main culprit was the "religion" aspect.
Bajorans on a whole were not interesting to casual fans imo, "Prophets, Pah-Wraiths" I thought DS9 spent a lot of time on them to no avail. As a hardcore fan, I can find that part of DS9 interesting, but I could see the casual TNG fan who maybe watches an episode if he has time would be turned off by that.
I thought DS9 got a lot right, the action scenes and core cast were it's strongest parts, and it knew how to tell a story better than any other Trek in my opinion. Had it dropped the religious undertones and been a little more traditional in that aspect I think it might have had a better interest amongst the casuals.
But all of that is just my opinion.
I think the main culprits were a lack of an identifiable "hero" ship (early on) and Nana Visitor (which is why I only tuned in sporadically).

Nana Visitor is freaking brilliant. Just because you have some sort of hate on for her, doesn't mean that it's some sort of widespread phenomenon among the 90s audience.
But I think it's utter bullshit that a series that ran for seven years and 178 episodes was somehow "cruelly misjudged". Instead of trying to present a martyr complex, some fans need to simply be thankful that they got to see the story told in a complete fashion. When I think of shows that were mistreated my thoughts go immediately to Star Trek, Firefly and Arrested Development.
Firefly was cruelly screwed up by Fox. It wasn't "cruelly misjudged" by the public - it's called one of the greatest or even the greatest SciFi series ever on the regular basis (which is a real exaggeration - I like the show, but, come on).
Arrested Development was also screwed up/ignored, but when was it cruelly misjudged? Did you ever see/hear anyone say anything negative about it? All I've ever heard about both these shows were accolades, from the people who are actually aware of them. I've never heard/seen the "Oh, I haven't watched it/have seen 2 episodes, but I've heard it's crap because of *reasons*" kind of comment that you can still see about DS9. Even many very successful shows, movies, books and franchises are "cruelly misjudged" by many people who haven't seen them or have watched one and a half episode.
The only one on that list that can even remotely be called "cruelly misjudged" (or is it?

) is
Star Trek due to the perception that it's a show for nerds.
Plus the articles number one reason was laughable. It's essentially saying people didn't care enough to either plan to watch when it was aired or too lazy to set their VCR to record it. That means people simply weren't as interested in DS9 as other shows that were on.
No. It's saying that most other shows were episodic with no continuing storylines that you had to tune in every week at the same time to be able to follow; and therefore, people simply
did not have to be all that interested in these shows for them to be successful and get great ratings. And that mattered a lot in the 1990s, before the age of Netflix, Internet downloads and people watching the shows on DVD instead of TV. Shows with continuing storylines are only really flourishing now.
Even in the 2000s, SciFi was forcing Ron Moore to have more standalone episodes in BSG in order to supposedly attract new viewers. And even now, the popularity of shows like
CSI in all its versions,
Bones or
Castle and a bunch of other procedurals shows that episodic TV tends to get good TV ratings because people don't have to be as invested and can just check any episode whenever they want to.