One problem with your line of thinking, James: these are not autonomous flight platforms. They require a joystick jockey to keep them going. All it takes is some good intel on where in the wilderness the flight radio shack is located, some ingenuity, a pack of pissed off patriots, and you can take over those drones for your own purposes or at least make the control of those devices quite perilous for those who wish to do the job.
Not fully autonomous for now.
They are indeed getting more and more autonomous. They don't need to be fully autonomous, either - just self-contained enough to be able to receive broad mission objectives via satellite. The uplink centres to those satellites could be (or already is) behind heavily reinforced government bunkers - the kind that three-shot "assault" rifle-armed citizenry would be machine-gunned to pulp if they attempt to penetrate.
Besides, you are not going to be able to scramble highly-encrypted digital signals with anything bought off Radio Shack.
Think about it: Afghanistan's people are armed to the gills with fully automatic machine guns AND anti-aircraft weaponry. The drones fly in and out with little concern over being shot down. Granted, the comparison may not be fully apples-to-apples, but you have to account for the fact that they have a more deadlier collection of weapons at the hands of their civilian population compared to what the American "citizen" is allowed by the government to possess.