Doesn't it?
Fly-by-wire is not actually fly-by-computer with a pilot to aim it, more a system to replace hydraulics and cables to move the aircraft's control surfaces with a system of electronically controlled actuators. The amount the controls may be moved may be restricted to prevent forces being applied which exceeed the design tolerances of the aircraft. Similarly the aircraft may be aerodynamically unstable and a computer will be used to provide balance and trim, so the pilot can concentrate on managing the aircraft's vector.
True, however commercial autopliot systems don't start up aircraft, obtain clearances and then take off, so you would still be in the realm of either the government doing it, and the pilot baling out (leaving the door open, which would be visible) or having to hijack a plane and know how to re-programme the auto-pilot whilst in flight, in which case you might as well fly it anyway. Added to which, the navigation computers on passenger aircraft don't currently have the sort of in-flight correction abilities of a cruise missile, for example. Also the current GPS satellites are owned and operated by the US military - don't you think it likely they have a rapidly effective off switch, in case someone fires a GPS-guided weapon at them?
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