I've been thinking about this. (Why yes, I am geek, since you ask.
) In their own individual ways, each captain has been at least somewhat polarizing. I'd say Janeway was more polarizing than average, but each of them has been to a certain extent. For example, I have never really liked Kirk - well, OK, I liked him fine when I was 11, but once I got old enough to realize some other aspects of his character besides what cool adventures he has...euw. But I don't hate him - he's just not my favorite. For another example, I had no idea anybody could loathe Picard until I started coming here. None. I mean, I could see why somebody wouldn't want to have him for a boss, say - he would demand a lot, and that's not always fun (nor is it always bad) - but how could anybody dislike this hardworking, noble, dedicated man? Well, it turns out quite a few people do, at least if some of the posts in the various "Who's your favorite captain?" threads are anything to go by. And I know people who dislike Sisko, and of course people who dislike Archer. A lot, some of them.
So I think they are all polarizing, and the reason is that we all have very high expectations of our captains and so it's easy to disappoint us. But I do think Janeway is more polarizing, and yes, I do think her sex is part of the reason. Plus I don't think it helps any that she was in a show that some people dislike so much (this is part of Archer's problem too, of course). That surprised me when I started coming here, too - I can see not being crazy about Voyager, but I don't understand the loathing. At all. Jeez, there are shows infinitely worse pulling in huge ratings right this very second.

So I think they are all polarizing, and the reason is that we all have very high expectations of our captains and so it's easy to disappoint us. But I do think Janeway is more polarizing, and yes, I do think her sex is part of the reason. Plus I don't think it helps any that she was in a show that some people dislike so much (this is part of Archer's problem too, of course). That surprised me when I started coming here, too - I can see not being crazy about Voyager, but I don't understand the loathing. At all. Jeez, there are shows infinitely worse pulling in huge ratings right this very second.