I've seen this, It's not just San Francisco, NY has been having a battle about the heliport Downtown. Since you bring up the issue of widespread anti helicopter sentiment, how do you think EVTOL will deal will this problem? They have to build hundreds of new heliports around the country, I can't imagine them being closed off to conventional helicopters.
"Uber sees opportunities to use floating barges for these where rivers, lakes and bay areas are available, but other spots could include the top levels of multi-story carparks, or ground facilities in less populated areas".
If they make noise, then they'll most likely suffer the same fate as helicopter commuters. The only way to override the noise complaints is if the operation generates TONS of money, and they can buy someone off!
As for top levels of parking garages? Oakland has one of those (think it still says heliport on the side of the building). I used to park there whenever I'd go to the county recorder, the pad is still there (think it has an "X " on it now) and the elevator still has the "H" for the top button.