"When do you decide to wait for somebody who is running to a stop and when do you decide to just go anyway and leave them as they're approaching the bus stop?"

{Disclaimer: I am not an official spokesperson for anything except my opinion as a MUNI driver, San Franciscan, and daily passenger just like the rest of you sorry sods relying on MUNI to get us to work on time. If you figure out who I am, please, please don't tell my bosses 'cause I want that pension some happy day - assuming there's any money left in the fund for the lowly drivers by that time.}

The first point to make is that there isn't an official MUNI policy on this; it's pretty much up to the driver. The reality on the ground is that if a driver is behind schedule, or is cutting it close, there's a strong motivation not to wait.

Personally, if I see someone within reasonable distance of where my stop is making a real effort to get to the stop I'll wait regardless of my time on the schedule. I may complain bitterly inside, but I'll wait. On the other hand, if someone's three blocks or on the other side of a major thoroughfare and waiting for what I know is a long light, I'm not waiting. Mind you, I will definitely NOT stop once the bus is in motion and moving (or already in) traffic. That's just stupid and dangerous frankly it's pretty damned rude of anyone to expect it. But of course in our me-centric culture they do, and often.