There's a standard phrase in my country that, if literally translated, yields "unknown makes unloved". I think a main cause is that DS9 simply is not as well known as the other series.
Also, the DS9 setting is somewhat different from what is expected of trek: flying around in a starship having adventures, so that could put casual viewers off.
I think DS9 requires something of an initial investment to get to know the series -more so than the other treks-: you have to know something about the spirituality of the Bajorans, about the political structure of the Cardassians, Sisko juggling between his roles of Emissary and Starfleet captain, etc. All these things cannot be learned from just one or two episodes. Which is probably what most casual trek viewers would have given DS9 before deciding not to tune in anymore.
On the other hand, people who don't like trek in general aren't likely to watch an episode -- as it still says 'star trek' on the tin.
And of course, finally, there are those trek fans that simply don't like DS9.
