I think BART is generally tolerable, but you're dismissing how obviously fucking terrible the BART experience can be and regularly is. A lot of people aren't willing to deal with that roulette, nor should they have to. Other transit systems aren't this bad.
By the way freeway shootings in the Bay Area tripled to more than one every day and plenty of people still use the freeway.
It's certainly lower than other commuter rail (it's a metro after all), and especially lower than Caltrain, but definitely not out of the question.
FWIW people complain about sketchy people and odd comments on BART, but I've also been followed by a driver I merged in front of who circled the block, cut me off, tried to follow me home, then flashed a knife on me and threatened to shank me. Last year someone got mad at me on the freeway then brake checked me at an exit. As long as I use BART before 11 PM on weekdays I never really feel more unnsafe than I do when driving, but I also am not the type that likes to live away from people. I enjoy cities.
Embarcadero <-> Coliseum both ways.