That's a little disingenuous, the fastest train from SJ->SF is under an hour at peak times. If you are in Downtown SJ, you can be in Downtown SF in way under two hours, with nothing but your feet and the train ride. San Jose, however, is huge, so its surely possible that a slow bus ride from south San Jose could add 45 minutes to the trip.
It would be nice to have a train leave SF later than midnite, but having taken that train many times, the ridership level is probably break even in terms of costs, at best.
Improving the light rail so that people will actually ride it and that it actually is faster than buses will go a long way towards bettering the situation.
The light rail is way too infrequent, and the worst part is that it doesn't sync up with Caltrain. Why does the light rail not get to Mountain View ~5 minutes before the CalTrain to SF instead of ~30 minutes? The delay is maddening, just synchronize them! It's even worse at night on the way back.
It would be nice to have a train leave SF later than midnite, but having taken that train many times, the ridership level is probably break even in terms of costs, at best.