I don't think I am confusing anything. 

It's pretty simple. More men get hired because the men doing the hiring want people who look like them in the available spots. There are fewer women etc. in large part due to systemic  issues that we don't address by pretending they aren't there. 

You're pretending there is an actual meritocracy at work here, when there is not. The article has laid out some pretty convincing reasons why. Perhaps some more research on your part would enable you discover these systemic issues which you are convinced do not exist.