The thing about commuting by bike/transit in the Bay Area is that it is doable, largely because there is critical mass with regards to enough people doing it that the facilities exist. In many cities, you cannot bring a bike onto a rush hour train. Here? 2 bike cars per train, packed to capacity. This summer, I was commuting from SF to Stanford. 10-minute bike ride on one end, 5-minute bike ride on the other end, 37 minute train ride in the middle. Got plenty of reading/homework done and a bit of exercise.
He's talking about Caltrain. If you can do pure Caltrain + cycle it will be faster than driving during rush hour, often significantly so, except on the one day a month that someone is killed, on those days you're fucked but at least you have a good excuse.