Except it is paid for. The buses pay the city to use the infrastructure. What is this infrastructure you ask? It's a space on a street. When it is vacated, the city bus, on the rare occasions it's right behind a google bus, will move in and "use the infrastructure." More often than not it's the other way around because city buses are slow, ponderous, and take a long time to get people on them.
Clearly you have not actually experienced this first hand.
First, there's the google bus, then the yahoo bus, then the apple bus, then the facebook bus and then the ea bus, and then the ebay bus, and during rush how it's a mess (according to a friend of mine who used to live near Van Ness and worked near the Financial district and used to take Muni)
In the southbay, in Sunnyvale near me, a particular Gbus is parking in a VTA bus stop and waiting for a Caltrain connection nearly every day. Sometimes they get their early and wait jamming up traffic while they wait for googlers to try to get off Caltrain and attempt to make a timed transfer** I've seen VTA busses stuck in the long line of traffic behind me and I wonder if every time they did this they might cause a VTA passenger to miss their Caltrain connections. I guess it's tough shit for the VTA bus rider in this situation, because they Gbus schedules aren't public knowledge...
AFAIK, SF is currently charging $1/day for a stop. If you happen to be an uber or a tour bus operator, you would have to pay a $279 dollar ticket for doing something like this. To scale this, it's $2/person to ride muni, but only a $100 fine if you are caught by one of the 2 fare inspectors checking 1000 busses (okay, that's an exaggeration). Not that $4/stop would break their bank, but to say they these busses paying their fair share is a bit farcical, they are getting a golden deal that most uber and tour bus operators could only dream about...
The VTA (in the south bay) hasn't started charging google yet. Probably because google bribed Mountain View with some free shuttle busses (however, they only agreed to pay for the shuttle busses for 2 years). I imagine that will turn out to be even net worse because now people will get used to the shuttle, and demand that it not be terminated after the 2 years is up leaving MV footing the bill. Meanwhile, google is probably banking that all the furor of the busses will die off by then...
FWIW, here's a purported map of the problem areas on the SF side...
***note VTA doesn't have timed transfers, so if Caltrain is late, you miss the bus and have to wait for the next one. Likewize if you bus is late...