> I don't want to automatically get turned down for a job because a woman applied. I don't want to automatically get turned down for CS help because I am the wrong gender.
Certainly! Nobody's goal is to reverse the historical situation so that men are systematically shut out of the field in some sort of vengeance for women being shut out for so long. A level playing field is absolutely the goal.
But despite all the progress we've made, there are still many, many places where women have to deal with negative biases as students, as job applicants, and as employees. Women still routinely face exactly the sort of bias that you're concerned about, except that it's no longer socially acceptable for people to admit (even to themselves) that they're doing it. (Different industry, but there was a study not long ago that conclusively demonstrated subtle but meaningful bias against women when hiring science lab techs: fake applications with female names were rated lower than identical applications with male names, by men and women alike.)
So my understanding is that when a company or college explicitly states a policy prioritizing women for help or hiring, they usually hope that this overt boost to female applicants will just cancel out the invisible but just as real biases against them.