For whatever reason, there seems to be a lot of enduring controversy and misinformation (or at least questionable interpretation) surrounding this issue. I will attempt to summarize some of the key points as I understand them.
First, DS9 was not a poorly rated show. It was simply a ratings disappointment compared to TNG, as were all the other TNG-era Trek shows. However, compared to its peers, such as Voyager and B5, its ratings were good.
Whether or not it was actually a more popular show than Voyager is open to debate, due to the difference in how the shows were aired, but anyway DS9 was approximately as popular or a bit more popular.
There was, however, a clear difference in how the two shows were promoted. DS9 was never intended to be the franchise standard-bearer on television in the wake of TNG: that was supposed to be Voyager, which was also the flagship show for the newly created studio network, UPN. Thus, Voyager was more heavily promoted than its syndicated counterpart. This, along with a few related incidents (such as Sisko and DS9 not being featured alongside the other shows and Captains in the marketing for ENT), has certainly contributed to the lingering resentment that is sometimes voiced by fans of DS9 toward the studio.
However, in my personal view, all fans of DS9 should be grateful for the relative neglect of DS9 on the part of the studio, as this is what allowed the DS9 creators to have more freedom to experiment. Doubtless they were a creative bunch in any event, but they also had to deal with relatively little interference on the part of the studio. Had the show been perceived as the standard-bearer of the franchise, a lot of that creativity would have undoubtedly been surpressed, and the show would have ended up being a lot more sterile and formulaic, i.e. more like Voyager and ENT.
On the subject of Rick Berman, while I don't think there is much to complain about regarding his involvement in DS9, I don't think there's much reason to praise him for it either, since he did very little writing for the show (perhaps none at all?) following the pilot, which he co-wrote with Michael Piller. Piller and then Ira Steven Behr were the showrunners. Prominent writers included Piller, Robert Hewitt Wolfe, Peter Allen Fields, Behr, Rene Echevarria and Ronald Moore. Berman is sometimes credited for pushing the idea of the Dominion to give the Gamma Quadrant an identity, but beyond that he doesn't seem to have been deeply involved with the show creatively.
Finally, as others have mentioned, DS9 is an extremely popular show among fans, and increasingly so. Deservedly imo, but regardless, its reputation has certainly not diminished among fans since it went off the air.