Although I have a tin foil hat for each season, the fire is really much to do about nothing. At least once a year there is a track fire of some sort at both Penn and Grand Central that causes a lot of smoke and shuts down the system for a while. I will say, however, that NYC is very, very tight -- the tightest I've seen it since the days following 09.11. I was down there on Wednesday and everyone seems on edge, particularly the police and National Guard, who were carrying heavy duty weapons with live ammo. (I know the ammo was live because a friend of mine is a special ops officer with the NYPD told me so.)
The sad fact remains, however, that there is very little that can be done to stop a motivated person from committing an act of terror unless you have good intelligence before the operation is set in motion and a lot of luck on your side. More people use the NYC mass transit system (Metro North, PATH, LIRR, Amtrack, and subways) on a daily basis than live in all but our largest cities, and without advance intelligence, there is very little that can be done to stop a person from getting off a train in Grand Central during rush hour and pulling the cord while in the middle main terminal.