You are correct. It will all come to this eventually. I believe, unfortunately, it will happen when more Americans are slaughtered in the US. On your last point, if I have a bomb in a bag, and I know it will be searched. I will not board the subway. I may go elsewhere, but it will deter me, and therefore secure that particular subway from my particular intent.
If you counted all the entrances to the subway system in NYC you'd realize that to secure all those entrances would cost more than operating the subway system in the first place. A terrorist with a bomb in a bag will simply enter at an unsecured entrance. Net result of the searches is that peaceful Americans get hassled while the terrorist is not deterred in the slightest.