- increased throughput compared to highways due to lower volume per passenger (something the US is trying to achieve with carpooling lines),
- increased reliability (there are no train-jams),
- increased passenger convenience (no need to look for parking or do maintenance on the train you ride),
- increased passenger productivity (you can work or read on a train),
- ease of transition to green source of energy.
Advantages of the car over the train:
- greater flexibility (generally roads offer denser network than railways, even in Europe or Japan),
- car is much more convenient for families with children.
I love trains. I love driving. I find that the latter is much more fun and convenience in places where the former works well. San Francisco's 101 could be one of such places if Caltrain was more like SBB.
EDIT: one more important benefit of the train:
- increased safety (much fewer fatalities per passenger; also no need for a designated driver when you go to a party).