We have 5.6M average weekday riders, and about as much for the weekends ( Sun and Saturday). That's 1.7 Billion rides a year.. [1]
If that's what you consider "not working"...
Does it have its flaws? absolutely! But does it work? absolutely!
As someone who has visited the bay area yearly since 2000, a quick observation comes to mind on why mass transit doesn't work as well there... The crazy idea amongst "21st century" companies to stick to the 1950s model of the "company town" in the suburbs.. and well, BART not going a lot further down than it should.
Companies should be moving in droves to the east bay, were you can actually build transit ( and there actually IS some real transit infrastructure ), and two, you actually have land you can build buildings that are horizontally efficient... ( not sand land fill that doesn't support any decent vertical building )
[1]http://www.baruch.cuny.edu/nycdata/travel/mta-subwayridershi...