I live in Oakland and am frightened of taking BART after hearing many horror stories from friends. If I, a healthy man in his 20s, am afraid to take BART, imagine how intimidating it must be for women and the elderly.
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. People run reds here all the time too, which is scary on both car, bike, and foot. 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.
By the way freeway shootings in the Bay Area tripled to more than one every day and plenty of people still use the freeway.
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.
Embarcadero <-> Coliseum both ways.