At night, just make sure you take the AirBart transfer bus in OAK, not the AC Transit bus option, if someone suggests it. Most BART crime seems to be auto-related, in the parking lots. On the train, crime is usually limited to the occasional vagrant shouting oddities, or even more rarely, someone asking for money. Due to the infrequency of off-peak train service, they tend to be more crowded - if you feel insecure for any reason in your particular car, you can walk between them while the train is operating.