It only takes 5-10 min from OAK to the BART station. I've never had a problem at night, but I'm 6'4" 230lb and don't scream 'victim.' I wouldn't worry too much about it, since I've never been on a shuttle from OAK to the station w/ less than five people so chances you're not going to be alone.

I also wouldn't worry too much about taking BART from SFO to OAK at night, done it dozens of times and I've never been in a threatening situation.

If you take a taxi it's going to cost you an arm and a leg since we don't do any kind of taxi flat rates to landmarks in the Bay Area like other metro areas do.