Google isn't paying for the roads or the right to use the public bus stops. It's taxpayer money; not every taxpayer (an aging lady, for instance) might want their money to go towards making a Google Bus possible.
Google and its employees are taxpayers. Google pays corporate income tax to California. The fuel Google buys to run the buses is taxed by California; fuel taxes typically go (or at least are intended to go) towards funding roads. Google employees pay state income tax, sales tax and SF real estate taxes.
And are you sure private companies don't pay to use the public bus stops? These stops are presumably owned by SF, so if they wanted to charge Google to use them they could easily do so.
That gives them right to use the roads. In this case, the Google bus is no different than other private bus or shuttle.
I don't really buy this argument. That's why all nations have and pay governments and governments should care about providing an overall public transportation system that works. That's why employees and companies pay taxes. I can totally understand that companies want to provide for their employees to do better work, but improving the public on their own is definitely outside of the scope for most companies.
If we wanted companies to fix the infrastructure themselves, we'd get a situation kinda like in Snow Crash.
It seems to me like this should be in the interest of the employees as well. After all, what if I want to take a bus somewhere else on the weekend, or want to go somewhere with friends?
Maybe these aspects (community integration, public transit in general) are not part of your personal objective function, but that does not make the uproar ridiculous. It just explains why you personally do not care about it.