This doesn't just happen in the bay area though, a writer recently discussed this phenomenon for the Twin Cities.
There really is an issue with the light rail system not staying open until 2:15 or 2:30 am. There were two letters published on July 31 concerned with the "Minding the gap" article. The letters seemed to be arguing against the light rail staying open later and had some very weak points.
First, there were suggestions to take a bus or taxi. But the buses run once every hour or so at that time, so you'd have to wait until 3 a.m. if you leave the bar at 2 a.m. Also, if you've ever been downtown and tried to take a cab at 2 a.m. you'd realize it takes over 20 minutes to finally flag one down -- and when you do it's a very expensive ride home. Most people just want to use the light rail at bar close, get closer to their homes and take a cab from there.