Question: "Why do bus drivers pass up stops and what goes into the decision-making process?"

{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.}

There are a couple of legitimate reasons bus drivers pass up stops. The bus could be an Express or Limited bus, scheduled to pass up certain stops. The bus may be too crowded to safely allow any more riders to board the bus. Lastly, the bus could be on instructions from a Supervisor or Central Control to skip stops in order to make up time on the schedule.