You're definitely right on (2) and (3). I've used many transit systems across the world (including TransMilenio in Bogota and other latam countries "renowned" for crime) and I have never felt as unsafe as I have using transit in the SFBA. Even standing at bus stops draws a lot of attention from people suffering with serious addiction/mental health problems.

1) is a bit simplistic though. I don't know of any European system that would cover even operating costs out of fare/commercial revenue. Potentially the London Underground - but not London buses. UK National Rail had higher success rates

The better way to look at it imo is looking at the economic loss as well of congestion/abandoned commutes. To do a ridiculous hypothetical, London would collapse entirely if it didn't have transit. Perhaps 30-40% of inner london could commute by car (or walk/bike), so the economic benefit of that variable transit cost is in the hundreds of billions a year (compared to a small subsidy).

It's not the same in SFBA so I guess it's far easier to just "write off" transit like that, it is theoretically possible (though you'd probably get some quite extreme additional congestion on the freeways as even that small % moving to cars would have an outsized impact on additional congestion).