Personally speaking (as someone who watches very little anime and has mostly only seen the famous ones, like Spirited Away and Kiki's Delivery Service), I think only ~10-20% of the animes I have watched have had male protagonists. It is surprising to me to hear that protagonists in that genre are mostly male, given my own overwhelming experience, and I'm not totally sure I believe it.
If I say "she" when talking about generic protagonists in some Miyazaki films I've seen, are you going to say I'm wrong and should say "he" instead because some genre of anime I've never heard of is popular with some demographic I'm not a part of?
If that's really how you think, then do you also opine that we should say "she" rather than "he" when talking about generic human beings, seeing as women outnumber men? Somehow I suspect not.