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).
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
and Arrested Development
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.
At the end of the day, DS9 is much like any other version of Trek. It had its good episodes and bad. Interesting and not so interesting moments. People hiding beneath latex and thoroughly face palming moments...