Welcome, new Browncoat. There are actually two different answers to your question: the biased version and the non-biased version. The non-biased version is this: FOX cancelled the series due to low ratings. The biased - and more in-depth - version is that FOX greenlit FF initially out of a desire to get another series out of Joss, even though they clearly didn't understand what he was pitching. Despite not understanding the concept of FF, FOX put it on the air anyway, but then jury-rigged with the airing schedule so much - either through airing the episodes out of order or pre-empting the series entirely - that the ratings were low, which gave them the perfect excuse to cancel the series outright.
BTW, if you're interested in more FF, check out the link in my sig. It's not the same as more filmed FF, but it's about as close as you're going to get.
One of the reasons they were in a relative rush to go with FF was because they HAD to fill that slot, which was originally intended for the Singer/DeSanto BSG.