{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.}
Dogs on MUNI - some thoughts:

Official MUNI policy is that service animals may ride MUNI at any time, un-muzzled and free of charge, but must be leashed. There is no limit on the number of service animals that may ride on the same vehicle at the same time. During driver training, a full day is given to teaching us the rules regarding service animals. It breaks down to one simple sentence: Drivers may ask you if your animal is a pet. If you respond that no, it's a service animal, the discussion is over. The driver may not question you or ask for any further documentation to prove that what you claim is true.

Unlike service animals, pets may ride MUNI but must be leashed and muzzled or fully caged and do not ride for free - the fare must be equal to that paid by the owner. Also, only one pet may ride on a vehicle at a time. Pets are not allowed to ride from 5am-9am, and are again barred from 3pm-7pm - i.e., commute hours.

Now let's talk about what really happens. I apologize in advance if this becomes a rant, because this is a subject that annoys the crap out of me and I'm liable to lose all restraint on the topic.