You're ignoring that the average ride on Muni, Bart, or AC Transit involves someone who's visibly or audibly tweaking out, loudly muttering curse words or threats to themselves / others, blasting music in the back from a tinny phone speaker, carrying a bag of cans and/or trash, or smelling offensively bad. It's no wonder that people won't want to take transit.
Source: someone who takes transit almost daily and has seen a LOT, and has received death threats on the bus twice in one year.
Meanwhile, here in India, where there absolutely are valid questions over the behavior of general public as a whole, particularly over freeloading, crowding, decorum and cleanliness issues: I don't think there are many tweaking, curse words or death threat complaints going around in public transit.
Source: someone who takes transit almost daily and has seen a LOT, and has received death threats on the bus twice in one year.