They are not paying for permits. The MTA has proposed a permit system for a limited number of shared private/public bus stops, but it has not been introduced, voted on, or even released publicly, and has lingered since as early as October 2012[1].
Even if the pilot program succeeds (maybe some time next year), and Google, et. al., start paying for bus stop permits, there's still the issue of the city turning a blind eye to all the illegal stops that have gone on for the last 5 years or so.
It's great for the city to create a program that encourages mass transportation, but subsidizing it for only a select class of people is a poor use of public funds at best, and discriminatory at worst.
[1] http://www.sfexaminer.com/sanfrancisco/rules-proposed-for-co...