Here's the question:
Do cops ever stop a Muni driver for anything like speeding or running a red light?

In theory, yes. In practice, no. Or at least, I've never seen it or heard of a MUNI driver getting at ticket while behind the wheel of a bus. I did hear rumor, one time that somebody got a ticket for not stopping at a live railroad crossing. There was a bunch of literature around the barn warning that Amtrak police were ticketing drivers for not stopping at the crossings, whether a train was coming or not. We're supposed to stop and open the doors. Mind you, this was just a rumor and some forgettable post-ups at the barn.

I will say that a cop would absolutely ticket a MUNI bus for, say, running a red light. Beyond that, I'm not sure. I don't think so. Meaning that yes, MUNI drivers are probably getting away with very minor traffic infractions that they average driver will likely be ticketed for-- especially if she's driving something hot like a red Ferrari.