I think part of it is that the types of shows that tend to have multiple important female characters are not the type of sci-fi/fantasy or procedural shows that fandom tends to enjoy watching collectively. And if you do get multiple main female characters in a sci fi show, they often fail the Bechdel test, episode to episode. So, you either have to convince people to pay attention to pairings where at least one of the characters is a minor character, or you have to convince people to watch shows that aren't the sort they tend to watch fannishly, or you have to convince people that they should ship two characters who don't have much canonical interaction.

Any one of these can be overcome for some of the people some of the time, but I think it makes it difficult to have really big femslash pairings, and, in fact, the one really huge femslash pairing I can think of (Xena/Buffy) had none of these strikes against it.