dazdaz - Possibly, but if the software for the flight was fully self contained then how would the aircraft be able to cope with en route changes? Just simple weather avoidance would be a problem, as would level changes for conflicting traffic, taking up the hold when stacking for arrival and so the list goes on.
Despite being dismissed as a factor by a previous poster I still maintain that security will always be the biggest obstacle. Lunatic terrorists taking over a ground control station, by any means, could bring unmanned aviation to a stand-still over night.