It's simply because most of the time, the girls are nuisances. If it's a fujoshi girl, it's fine. But if It's a girl that threaten the relationship that we ship, then we hate them to death. And in my own opinion, most anime or manga girls are annoying. I just find their cutesy personalities disgusting. Example: Shiemi from blue exorcist. She annoys me. Don't know why but I just feel annoyed by her. She is so freaking pathetic and weak that she depends on a freaking plant for strength. Getting back on topic- Female manga characters in BL that aren't side characters or fujoshi, are most likely to be hated.
I feel you...the one that annoys me the most, to the point that I stopped watching the anime, is Orihime from Bleach. Here she has this awesome power. And yet SOMEHOW her @$$ is always getting kidnapped. Really? "Oh no, Ichigo save me!" Man up and save yourself, you ninny. Sheesh, those powers were wasted on you. Your best friend kicks more butt without powers than you do, with. Argh (fortunately since I stopped watching, I came across some very interesting Bleach djs...nuff said)
But yes, most females in BL are created to be hated.
That bitch, why is she in existence. She should just get run over by a damn bus! *throws phone across room* Fuck, shit, cupcake! Why'd I do that? *climbs off bed* please be ok please be ok.*picks up phone* Phew! I didn't break this one. Mom would've crucified me if I did.