We have all had the madonna/whore complex imposed upon us in different ways, both those of us who create the characters and those of us who evaluate and react to them. Deciding that some female characters (love interests and damsels in distress) are Bad Models Of Women, while others (ass-kickers and tough loners) are Good Models Of Women, only reinforces this. Like who you like. Be receptive to others' different views of these characters, though.
We have all had the notion of Woman As Other imposed upon us in different ways. Handwringing over how people should write more fanfiction about female characters as some sort of charitable gesture only reinforces this. Write what you want to write. But step outside your comfort zone now and then and challenge yourself; you might find you enjoy something you didn't consider before.
I took a look at what characters and pairings I end up writing about and the biggest pattern that emerges is randomness. Ask me for my top five pairings, then ask me for the five pairings I've written the most fic for, and you'll get different answers. I haven't written any fic for Garak/Bashir or Zoe/Violet, and they are up there. I've found that what matters more than how much I love a pairing is how engaged I feel with the fandom.
My most-written pairings, for the record, are Lockon/Tieria and Sasuke/Sakura by a huge wordcount (I don't write the latter anymore, because I'm no longer engaged with either the canon or the fandom). One is slash (or genderqueer depending on who you ask) and one is het. I have never seen fans pass a moral judgment on the slash pairing--a value judgment of "omg this is so canon ^__^" or "God, I'm so sick of this stupid baseless overrated pairing," sure, but not a moral judgment. The het pairing? Last I was in fandom, it was constantly looked down upon for being a Bad Model Of A Relationship, just as so many female characters are looked down upon for being Bad Models Of Women. You were considered a better, more enlightened fan if you shipped slash or a het pairing that lined up better with Western feminist expectations of gender dynamics, regardless of its other flaws or canon evidence. I wonder if that's a pattern in het pairings vs. slash pairings? Come to think of it, in my current fandom, the pairing I saw called "incestuous mental pedophilia" with no evidence to back up the claim is het (and does have problematic elements, like all male/female gender dynamics, but incestuous mental pedophilia is not one of them).
A meme I've just seen emerge from the last round of is-slash-(appropriative/progressive/writ
Comment with the name of a female character and I'll tell you why I love her.
Edit: Oh, yeah. My comments on a previous round of this discussion can be found here.