South Park makes fun of all types of people, ideas, social things. Blame the people that take that song super duper seriously rather than a satirical, not super duper serious cartoon.
The issue isn't really South Park, it's how it's being brought up (on GAF for instance) constantly as if it was some sort of insightful debate closer. I didn't watch SP in a long ass time but I'd say it did go "politics" quite a few times, like with that voting stuff in school with the douche and turd sandwich, and often SP have this weird non-commital stance of putting every side back to back and standing for a somewhat unfeasible middleground.
I think one way things play out is that the issues, terms, concepts, etc. all exist prior. I've seen "safe spaces" discussed and mocked for probably five years now. But most people are ignorant of the issue, either pro or con.
When South Park mocks it, the people involved, etc. for 20 minutes as part of a story, even if they don't take an obvious side, it's the first introduction some people get to the concept or the first significant one. A GAFer might have seen "safe space" threads before but ignored it or not really understood, then they saw South Park and now they're an expert. (When I think both Parker and Stone would admit they don't deeply or even lightly research 95% of the subjects they take on.)
So then it becomes partly a fight over South Park's portrayal and the whole "it's comedy!" bail out angle.
I feel like getting mad at anything South Park does is either missing the point or playing into Parker/Stone's hands.
Like the dude who played Chef getting butthurt over the (rather tame) scientology disses after the show had been sticking it to religion in general and Christianity specifically for years.
They've strongly suggested since that they don't believe it was Hayes (who had had a stroke) personally, but "his people"/Scientology's people behind it since he hadn't minded them poking fun at Scientology and other things before and said so to them. And either Parker or Stone said that it's one of the South Park moments he regrets since they did it in anger the week of rather than having more time to mull it over. (When he died a year or so later they put a dedication card to him at the end of that weeks episode.)