Because the politics of the rich don't make good infrastructure for common use?
So, BART was originally constructed for the purposes of suburban commuters heading into San Francisco for white-collar work with generous no-travel times baked in for maintenance. It's why there's no track duplication: if you're shutting down fully for hours you have plenty of time to work on maintenance. Almost immediately this assumption proved false, the hours got extended but the basic design is still in place. And, if you're really, really rich here you'd pay someone to drive you. Why futz with the BART? All you, the rarefied wealthy, need to do is keep BART limping along just enough that the service workers and middle class white-collar people and what not you rely on can get to work.
It's how we get BART, it's how we get a serious housing shortage.
Because it's a public service and it doesn't have incentives to get better. It also has no fair competition from the private sector, given the amount of money in infrastructure that was spent on BART is unmatched.
Look at how much private transportation improved (taxis -> uber).
Besides, BART is the last of SF's problems, I'd rank homelessness and crime higher.
As I always say: One of the richest parts of the richest state of the richest nation on this planet and we have ... BART. How is this possible?