Until then, I'll always prefer driving/walking/biking/anything. Unfortunately, I'm in a situation where I can't drive now, and I have to deal with an awful San Francisco public transit system that does 0 of the things I listed.
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.
But now there are a ton of pretty awful immigrants from the Middle East who harass women, destroy property, and threaten anyone they dislike... which is quickly making European cities very unpleasant places to live. I wouldn't be surprised if Europeans start their own version of white flight away from their cities.
On many bus routes the conditions can be positively third world. Graffiti everywhere - seats, floors, windows. Human excrement. Urine. Addicts. Homeless. MUNI buses are one of the less fortunate places you can find yourself anywhere.
Having lived there in the past, I can sympathize with residents who want to drive, or take Ubers everywhere. The public transit in the city can be a very foul experience - though this is largely a reflection of the city rather than the system itself.
We focus on crime, because it's easy to lash out at order breaking down and can relate to being harassed by the small percentage of Muni riders who can genuinely be considered subhuman refuse. In reality, though, SF has several times as many annual traffic casualties (around 3000, from some rudimentary Googling) as crimes reported on Muni (around 1000).
That latter figure has some factors that may suggest undercounting (it's reported crimes, and I can see how people might have so little faith in Muni that they don't bother reporting it) but also some that suggest overcounting (it includes fare violations and eating on the bus).
Muni certainly needs to be cleaned up, but let's not get ahead of ourselves: you're much more likely to die via automobile in SF than being shot or stabbed on the Muni. I wouldn't be surprised if you're more likely to be killed being hit by a Muni than murdered on the Muni.