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.
The Afghans also have an advantage that is impossible in America: A tribal command structure with a degree of family loyalty that is impenetrable.
"Honor your father and mother, THAT YOUR DAYS WILL BE LONG IN THE LAND THAT THE LORD THY G-D GIVETH THEE."
People go to church, blather the words, and have no idea what they mean.