On some level I agree with many of the sentiments expressed in this thread -- that DS9 was "ahead of its time"; that audiences in the mid-90s probably reacted against it worse than audiences today probably would -- but it can't be denied that, for whatever reason, DS9 was
less popular than TNG. I think this is just the luck of the draw though. The trouble with spin-offs is that risk of decreasing returns. Its possible that any
follow-up to the massive success of TNG would have been given a (relatively) lukewarm reception.
Personally, I appreciated DS9 at the time -- heck, I appreciated VOYAGER at the time too -- but I can also see why there were some quarters with who DS9 just didn't "take".