The reason is very simple. Much less girls play competitive games then males. And no, you cannot cite that one study that shows females make a substantial amount of gamers, because that study focused on all games, including very casual stuff.
As for so called misogyny in the gaming sphere, that's just bullshit. Just because someone uses a gender targeted insult towards you doesn't mean it's misogynistic. If anything, I'd say girls get very much preferential treatment when it comes to games, but I'm not gonna claim that's a fact, that's just my opinion based on anecdotal evidence.
The reason why tournaments that feature only woman get lesser prize pools is also simple, they don't have as wide of a reach when it comes to audience, so the sponsors make less money out of sponsoring them (yes, sponsors make money out of sponsoring - it's called marketing), it has nothing to do with being overlooked.
And the last thing - most females just aren't as good in competitive games, I'm sorry, but that's often a fact. On average man will for example have faster reaction times Source and that's just one factor.
So please, don't bring gender politics into this. It's just as simple as this:
TL:DR
Less women tend to play competitive games.
Women are worse in competitive games on average.
RE: Gender Disparity in eSports