Okay, I just went out for smoke and had a thought. My answer lies in something that was touch on here briefly, that of public and private property.
If one choses to go on an airplane, I should be searched by government agents. Heck I could be searched by agents of the airport or the airline as I am entering their private property. But I think the bigger issue is the question whether or not some else, or their private property will be damaged in the case of an explosion, and whether or not they had a reasonable opportunity to remove themselves from that threat.
People are free to choose whether or not they wish to use either method of transportation, and to take the risks associated with it.
However in the event of an explosion on the plane, or the plane being used as a weapon, the private citizen has no practical way to not be killed by debris or the plane hitting their building or what not.
While in the case of the subway, knowledge of their routes are readily available, they are underground so debris proably wouldn't be a factor and if the private individual feels that it might be they can move. Where airplanes are much more mobile and one can't predict where it's exact flight path would be. In one case the citizen can in essence protect themselves, in the other the citizen can't.
