I've been rereading Julie Phillips'
biography of James Tiptree Jr. and she does a nice job describing how Tiptree/Alice Sheldon demolished the idea that men and women write differently. But another question is the one being asked here: do we prefer male or female protagonists?
There does still seem to be a perception that science fiction fans tend to be male, and a growing notion that fantasy fans are more and more often female. I think this is an oversimplification, personally. It is true that before about 1970 most science fiction was marketed towards young men, and there were some male fans who didn't want women to be writing science fiction, or even reading it. Those days are past now, thankfully.
What I see today (and this may just be me) is a struggle to write strong female characters who aren't just men in disguise. This seems particularly common when women are presented in traditionally male roles like warrior. One of the reasons the early seasons of
Buffy the Vampire Slayer were so good was that Buffy was so very typically female (yes, she wanted to be a cheerleader; how stereotyped is that?), and yet still fought, literally, with evil bad things. She didn't have to surrender one part of herself for the other.
Then there's the question of writing stereotyped female characters who aren't like the boys but who are still strong characters. This can be particularly difficult work to find, since it requires the author to balance his or her character in societies that are usually at least a little sexist. The best example of this that I've seen is
Ursula K. LeGuin's Tenar, from her
Earthsea novels.
This leads my free-association post to the question of the use of science fiction to consider gender roles themselves, including ideas about passivity and strength. A novel I've just reread is
Karen Anne Mitchell's The Usahar, which has a strong female character resisting aliens who want to reduce her to the stereotype of the passive woman. It's an edgy book and it made me think, which are two things I look for in what I read.
Anyway, these are some of my thoughts on the subject of gender and science fiction. It's a big, fascinating topic.