I'm living and working in NYC now. I have been through a few bag searches entering the subway. The cops basically just peek in. The have never rummaged through the individual items. I carry enough junk in my knapsack that if I wanted to sneak a small bomb onto the subway, this search would probably not have stopped it. Also, a friend of mine on the NYPD tells me that if they do find illegal substances or items unrelated to terrorism, then yes, they will make an arrest. But on the other hand, I haven't seen anyone arrested or heard of anyone being arrested at the bag checkpoints. It looks to me more like the cops just want to make their presence known, and keep the bad guys guessing.
IMHO they are violating my fourth amendment rights. I've read the cases cited by benjammin, and it seems pretty clear the authorities are out of line, but since I don't have an extra $250,00-$500,000 to take the case to the Supreme Court, my only real choices are to refrain from carrying illegal items on the train, or take a cab.
As for searching people after they have boarded a train, that seems to be an even more egregious infringment of the fourth amendment than the false "choice" they give you at the gate.
So here we are. Bag searches that won't stop a determined bomber and incremental infingement of rights (so we get used to it?).
Hopefully, the government isnt organized enough that this is a grand conspiracy to deprive us of our rights. More than likely, its buraucrats running around saying "we have to do SOMETHING." Even if it is totally ineffective. We'll see.