The answer to this one is actually really simple and comes about in two parts:
The first part is that ‘male’ is the default gender for characters.
The second is that no one wants to condone violence against women. No one who isn’t a huge douchebag, anyway. Additionally, it “doesn’t make sense” for a woman to overpower a man, which the protagonist may well be, especially in contests of strength.
The thing about the Final Boss type character is that the audience needs satisfaction and in many cases, satisfaction means poignant death. And poignant may mean ‘horrible’ or ‘brutal’ or ‘violent’. Audiences also like to see the bad guy, if truly terrible, thrashed. Think about your favorite fight scenes between hero and villain, swapping sword blows, punches, bullets…Now imagine that the hero is a man and the villain is a woman. And you see one major problem. A man cannot stab, punch, or shoot a woman, no matter how evil and vicious she is! It’s just…wrong! Especially in the light of actual domestic abuse, which is a real thing, and actual murder of women, which is a real thing, and actual shootings of women – and those things we all agree are very not okay and here is this story with its female villain where the woman is stabbed, punched, shot, and it is okay and even good? That can’t happen. (And obviously violence against females is the worst kind, worse than violence against males and violence against children just doesn’t exist because it’s too horrible.)
Villains often need to be cruel and awful, horrible people. Consider what a hard time people have with separating a single character from their entire group – race, gender, sexuality, religion, etc. This is true in real life as in fiction. One Muslim is a terrorist, bam, we think all Muslims are out for American blood (despite the fact that their religion generally does not actually condone violence). Pearl Harbor? Better put all the Japanese into our own concentration camps of sorts. Consider also that people have a hard time separating a character’s views and behaviors from the authors – if the hero is a gigantic homophobe, people will generally assume the author must also be homophobic. Authors and books have been picked apart for their social messages in what the book/writer is saying by what they hold as ‘good’ as embodied by their protagonist and protagonist’s growth and what they label as ‘evil’. If you have a woman villain, the hyena critics will wonder if you did that because you think all women are evil, all women are heartless and cruel. You’ll find people wonder if the villain stabbing the hero is symbolic of an ex-girlfriend or a traitorous female friend.
This sort of analysis of your story will happen anyway. But do you really want people criticizing your view of women, especially in today’s heat of the subject? Where there are “feminists” who will find you like a laser-guided missile and beat you into oblivion? No. You don’t want to do that. Better stay on the safe side and just pick a male villain.
Is that just today’s society? I remember learning the actual story of Hercules in fifth grade and becoming very irate to learn that, once again, Disney had outright LIED to me about a story. (I still kind of hate Disney for miss-telling stories…but I do like anything original by them. I even like Tangled, as it seems to me more a presentation of their version of the story th- getting sidetracked, sorry). I asked my mom why they did that, why they felt like they had to make Hades the villain when Hades is actually a perfectly nice guy except for that part where he kidnapped Persephone and does not actually show up in the story of Hercules at all. No, don’t argue with me – Cerberus and Charon do but Hades DOES NOT.
My mom said that it was probably because Disney did not want to portray a woman as a villain.
Now as an adult, I think it’s because Disney didn’t want to tell a story about a godly fellow who cheated on his wife and his wife spent the rest of the child’s life trying to ruin it. Why make Hades the bad guy instead? Because he’s the god of death and the underworld, CLEARLY he’s totes evil (even though it wasn’t his choice to be such, he lost in drawing straws with Zeus and Poseidon).
But my mom’s answer is curious, don’t you think? Because Disney TOTALLY avoids all female villains COMPLETELY.
Rescuers? Emperor’s New Groove? Snow White? Cinderella? What’s the difference between them and Hera?
Well, nothing – I think my mom just got the answer wrong but didn’t want to bring up the whole adultery thing with me as a fifth grader even though I clearly knew about it. But what’s the difference between these women and others? In a fairy tale’s case, there’s two big points. One, the protagonist is female. So it’s all good, women can totally fight other women. No male domination there! And no worries about any inadvertent messages about women: look, the girl lead right there shows we don’t think all women are evil! Two, these women villains don’t tend to be…women. They’re evil witch-fairy-whatevers. I mean, you don’t really think so much about a boy dragon being a boy; you think about it as being a dragon. Yes, witch-fairy-whatevers are humanoid lending to think more easily of them as being a woman, but really, when you see the evil crone bent over her staff with a flapping raven, do you really think of her as a woman? They’re all female, so it’s more like a racial trait than an additional trait.
So how do we fix this problem? (Honestly I don’t think it’s a problem but clearly people want to see more female everythings so let’s address it.) First, we do have to remember to separate author from character from group – just because a man writes an evil, devilish, manipulating woman does not mean he thinks all women are like that – and neither does the book. Next, you’re just going to have to get over the violence against evil women thing. Although really, it does come back to the violence against men and children – the ‘against women’ part isn’t the problem, it’s the ‘violence’ part. If violence against a female villain bothers you, reevaluate how your characters handle ALL violence. Maybe you should pull an Asimov – “violence is the last refuge of the incompetent” – and have your heroes fight the villain some other way. ‘Cause you know what? In real life, violence against anyone is inappropriate, although against an assailant sometimes necessary to some degree for survival, even a female assailant – that should be the same in our books.
Here’s the most important way to fix the problem, though – male characters are generic characters in part because of androcentrism…and in part because I think most people, especially male writers, find them easier to write. Practice writing good female characters, real women characters, and you can make one evil just as well as heroic.