The FAA heavily regulates aircraft due to the extraordinary disasters that can occur as a result of midair collisions. Drones are aircraft that any asshole currently can fly just about anywhere. My son and I have a DSI Phantom and it goes VERY high and can be flown at great distances from the operator. While I am not too hip on government regulation, it is not hard to see how these things can be used for mischief. Moreover, I do not want to die in a firey plane crash because some jackoff decides to have his (I say "his" and not "hers" because this is the kind of stupid shit only a guy does) drone play chicken with a plane on which I am a passenger while said plane is attempting to land or take off.
I see no analogy with firearms and the second amendment. While I think the second amendment ought to give us unfettered access to all small arms, including automatic weapons, armed drones in the hands of regular citizens seems a little out there. Yes, it is happening and I don't necessarily think it should be outlawed. However, if you fly one close to me and start popping off shots close to me then don't be surprised if I return fire and take it down.