Mountain View and Cupertino, at least, seem to behave relatively sanely. Santa Clara almost goes too far as an industry town.
At the core of it, these people have a xenophobic fear of change. They might be making noise about rent prices now, but if these companies tried to address this concern, the concerns would shift.
The problem is the Peninsula actually is boring, at least for single people who don't drive. I'd rather see SFBA tech contribute $10-20b on making the Peninsula an awesome place to live, rather than trying to fix SF's infrastructure and politics. Plus, there's money to be made doing it.
Imagine what the SF housing/policy landscape would look like if these companies double headcount over the next 5 years. What's happening with the buses will pale in comparison (and the worst part is the buses aren't even the issue, they're just visible).
1) Large voting bloc of employees
2) BATNA to getting their way: credible threat to move. Google can't credibly threaten to move out of SFBA, sadly, and Twitter couldn't credibly threaten to move to Brisbane (because, Brisbane is crap). If Twitter hadn't had crazy political connections, mid-market wouldn't have happened.
You don't get large amounts of power just by paying a lot of taxes or employing a lot of people; if there are big voting groups who dislike you, you're still screwed.