A few things:
I´m quite sure that terrorists will look for security leak. You mentioned the subways: It has been tried in Paris, France in the early ´90s when Algerian terrorists set off bombs in Metro stations and public places for several weeks. In the end the French government removed dust bins and had sever manholes welded shut, and they let military patrol through those places, just a step short to declaring martial law. Eventusly the perpetrators got caught.
On another website ran by hobby gas turbine builders a while ago I found a discussion about how easy it would be to build a home made cruise missile for less than $20,000 out of readily available material, including a GPS receiver, which could be launched in a rural area and then fly 50 miles beneath the radar coverage to a target, carrying a payload of 50 kgs. Imagine this to be filled with a biological or chemical warhead. Money is no problem for the current generation of terrorists, unlike their communist or nationalist precedecors in Europe (Red Army Faction in Germany, IRA in Ireland, ETA in the Basque country, Red Brigads in Italy), who had to resort to rob banks for funding.
Then, even if yiou have fighter cover, if you shoot down a large jet over a populated area you´ll kill a lot of people on the ground.
Earlier this year a mentaly deranged college student stole a Katana from a GA
airport close to Frankfurt (FRA
) and threatened to crash himself into the bank buildings (Frankfurt is Germany´s business captital with a skyline imitating NYC), wanting to remember the late US astronaut Sally Ride (who died in the Challenger explosion). The Luftwaffe sent two F-4s up to cover him.
Now imagine the damage caused by this light plane crashing into a building with it´s approx. 500 kgs, and 40 liters of uel on board. You could as well crash into the Empire State Building with an ordinary car, no big damage to the building.
Now imagine the fighters would have opened up with their Sidewinders over the city: The rockets probably wouldn´t even have seen the target because the engine isn´t producing a lot of heat, hitting some building.
Or the 20mm shells of the F-4´s cannons would have ripped right through the composite plane, exploding again in the city.
An ATC controller managed to talk him into landing in FRA
, where hegot arrested. He´s been certified insane and was sentenced to be locked away in a mental institution.