> "Give me a public transportation system that runs on time, doesn't spread disease, doesn't have punk kids who confront you for no reason, is safe, and has sane time schedules and I'll be happy."
The problem is that you live in San Francisco.
The biggest problem in that list (safety/perceived safety) has more to do with the city than the transit system itself. It's not a brokenness in the transportation system (though more can be done to curb it, certainly), it's a brokenness in the society it serves.
It's always a little depressing to think about how so many other cities - both bigger and smaller - on this continent put the transit of San Francisco utter, complete shame.