Besides, when you say "control tower" who exactly do you refer to? Departure, arrival, mulitple enroute controllers, every controlled airspace along the route (Class B, C, and D)? On a cross-country flight you could have 100 seperate control towers. No thanks.
RE:Technology exists to authenticate wireless network traffic (e.g. RADIUS, going into Windows XP). That's to say, the plane's autopilot won't respond to anyone but the control tower personnel.