Their comfortable viewing distance is something like 12,000 feet, which is almost 3 miles up. You're not likely to have anybody shooting at them because they'll never see them.
That said, I agree that people will accept their new passengerless overlords, and it'll probably start in New York.
I suspect government drones will get federal protection if people try to use them as skeet targets when they fly over their property.
Countdown to when the public starts to say "oh well, what can you do, we need to be safe" (ala TSA).