It would be very difficult to fly a train into a metropolitan skyscraper.
Maybe I wasn't clear.
All this type of scanning, and pat downs, and taking off your shoes, is to detect explosives. You can't commandeer an airliner with an underwear or shoe bomb.
This is all about fearing an explosion. An explosion can occur anywhere and in many places that will sow more fear and economic catastrophe then on a random plane.