How come an unwell Patriarchal Society has harmed so many people?

Because there are actually some men and women who do fit in better with the standards of the Patriarchal Society.

And some of them decided it felt easier or more empowering for them to just go along with certain groupthink dynamics and cult mentalities because that brought them a measure of security and comfort and self identity.  

So, some of the "good" people ended up going along with stuff that ended up being pretty harmful to a lot of other people in the long run, just because they got short-term gains from going along with it.

They decided not to have very much empathy for other people who didn't fit in so well with the system.

It's good that not all people had the ability to go that way, though, because that is really not a sustainable way to live or to treat other human beings.