I think it's a good idea. The police never bother me and I don't mind putting my bag through the system. A few years ago I was in Korea when a lunatic set the train on fire and so many people died. Beijing is safe anyway, but the security on the subway, in my opinion, is a good thing!
The police are pretty good at weeding out the bad guys. They never searched my person with the wand or anything....
It's a lot better than Los Angeles where you'll get pulled over and searched just for walking down the street after 10 PM.