I commute to Manhattan on the subway every day, with a nylon briefcase on my shoulder, and have never been stopped once for a bag search. They hardly ever stop anyone, and I'm in the high-risk areas. I actually like the police dogs better, and I saw a few in Atlantic Avenue/Pacific Street (downtown Brooklyn) stations this evening. It's even better if the dogs are trained to sniff out bombs. There's a lot of suspicous people in that neighborhood, and many subway transfer points in that station, including the Long Island Railroad, so this makes more sense.

9/11 conspiracy theory debunking site:
http://us.geocities.com/debunking911/index.htm