I don't think that's it. I've spoken to other Trek fans in-person and, independently of each other, they always say "it didn't feel like Star Trek." The problem was that it's not set on a space ship and there's little to no exploration, which is a core theme of TOS, TNG, VOY, and ENT. You also need to watch DS9 and invest more time because there's more continuity - not that the other series lacked continuity, but you could not sit down and watch a single episode of DS9 the same way you could the other series.
Another criticism of DS9 is that it explores the limits of the Federation. There is more political intrigue. Rather than a single rogue officer storyline (Maxwell in TNG), you had full-on conspiracies in DS9 (Leyton et al). The Federation hides its failures (e.g. the genetically enhanced rejects being institutionalized against their will). You even have Starfleet itself agreeing to manufacturing evidence to trick another power into supporting a war. Section 31 also rubbed a lot of people the wrong way.
DS9 was very different from Trek shows before and after it, making it a little controversial. It doesn't help that the cast and crew of other Trek series shit on DS9. Shatner is a legendary asshole, Stewart was openly hostile on set for the first season, Jeri Ryan slept with Brannon Braga to get her role, and so on. That gets swept under the rug, but DS9 and Brooks is the outlier that... produced seven seasons without any weird controversies, except for Terry Farrell getting fired because she wouldn't sleep with Rick Berman? People make shit up about Avery Brooks to this day.