Oof. That totally blows. With that said, NYC is an exception, commuting is not nearly as bad there as in other places. I had an internship with the Port Authority of NY/NJ when I was in college, and I had a free place to stay in the Hudson Valley. I was able to bike to the train station and take a train to the city (Jersey City, that is :D) most days of the week, except for when I had to be there way early. The first train got there around 7, there were some days I had to be there around 6am. Commuting at 6am was not really that bad though. On the way back, I would drive over Bear Mountain, which is a gorgeous piece of land.
Also, this is going to sound stupid, but one of the best things about the train was drinking a 40 of High Life on Friday afternoons while I zoomed home. You can't really do that in a car.