There were a bunch of creative differences between the FOX executives and Joss Whedon. For example, the executives wanted to be able to put the shows on in any order they chose. Anyone who has watched the series knows that the pilot makes a lot more sense if seen first rather than the third or forth episode aired...
There are 3 episodes in the DVD that were never aired, so the final episode of the season (which was aired) actually had to be altered for certain things to make sense. It's changed back in the DVD collection, but what aired is included in the deleted scenes.
Having watched those 3 episodes, they all 3 have some stuff that could be considered questionable in terms of sex and/or nudity (two of them show bare backsides), so I imagine FOX didn't want to air them without cleaning that up. I don't know the history, but I imaging Joss resisted.
In the end, my understanding is that too many viewers didn't quite get it, in part because things were out of order.
At this point, it's escalated to what could be called a cult following. I just watched the entire series and the movie again as part of my recovery efforts