EDIT: Ok, I skimmed the article which pretty much lost my interest after "Any creature on screen minus a 'Y' chromosome tends to be a side player in this cinematic universe."
Why does this need to be a male vs female thing?
...because it is?
Even if one accepted your premise that directors are always hired based on their ability and no other factors (and I don't for the reasons Harvey cited), that quote is referring to the content of the movies
. If superhero films are overwhelmingly concerned with their male characters, with almost exclusively male protagonists and very often dealing primarily with the male characters, then that is a way in which superhero films are gendered.
If you want to say it's a good thing or a neutral thing, then fine, whatever. But it is a thing
, it is an observation that is empirically true.