That's for regional transportation. For local transportation, the New York City Subway is simply unbeatable. Reliable, safe (even at 3AM), and running 24/7, there's no other practical way to get around the city. While I live in Jersey City and have to take the PATH to get in to the city, it may as well just be an extension of the subway system (it takes different fares and is run by a different organization), running 24/7, safe, and reliable.
I don't own a car, and for regional travel, rail is the way to go. So with all this, am I going to Boston via train for the Summit and FUDCon? Nope, via air because of stupid Amtrak service disruptions due to the replacement of a bridge apparently.
Note that my opinion probably differs strongly from Seth's, since he's down in Raleigh and I'm actually in the civilized world (/me ducks :) ). Seriously, about two-thirds of the nations rail passengers live in NYC.