Even when female characters exist in canon materials, though, they’re rarely written in dynamic or compelling roles — in short, if they aren’t leads, then they often exist as an afterthought to the men, not alongside the men. For example, the BBC’s Sherlock has female characters, but the main characters are two guys, Sherlock and John, and as a result, most of the fic in Sherlock fandom is about Sherlock and John. Characters like Molly Hooper and Mrs. Hudson are framed by their relationships to the men, and thus may not hold as much potential for fanficcers as do the main characters. As AO3 Census creator centrumlumina says, often the most popular ships are born out of a canon rivalry, a best friendship, a divine bond — and most of the the time, these are relationships that men get to have.
I think the most compelling theory I’ve seen floating around is the one that says that fanfic authors, especially the 80% of them which are female-identifying, are societally conditioned to regard female sexuality or female pleasure as unimportant or undeserving of attention. Think about some of the non-canonically supported ships that you know. Mycroft and Lestrade have been in one scene together in all nine episodes of Sherlock, but Mystrade is a huge ship. In Teen Wolf, Stiles and Derek are constantly shipped together, despite sharing very few canon scenes. Meanwhile, Allison and Lydia, who are getting a lot of screentime together this season, have barely five hundred fics on AO3. (Sterek has about twenty thousand.) I don’t mean to disparage one ship or the other — what I’m curious about is why fandom seems to have latched onto the male ship over the female one.