The other thing is getting to BART - if you live in the Mission or within a handful of blocks of Market St; and your destination is in downtown Oakland or on th

The other thing is getting to BART - if you live in the Mission or within a handful of blocks of Market St; and your destination is in downtown Oakland or on the west side... you're fine. But if not, you need to coordinate your trip between BART and two different bus networks on either side of your train trip (or shell out for a car service / cab). Not only are train lines between Manhattan and Brooklyn much more plentiful, they fan out to a much larger collection of destinations on either end. It can be a one-system trip, which makes a big difference. BART isn't bad by any means, and SFMTA/AC Transit do a decent job, too. I've lived in Miami and around Tampa, two other large cities which do an almost immeasurably worse job with transit. But BART is still a very commuter-centric network for getting commuters from suburbs to downtowns, and isn't a substitute for a true local subway network. Thats where the stigma comes from, in my opinion.