Ultimately, your property "rights" are granted rights, not inalienable or natural rights. You don't own air rights or mineral rights for simple, pragmatic reasons.
Hell, by international convention "conquest" is the most sure-fire way to get more real estate.
As for noise pollution - people have been suing over that since the dawn of aviation. Sometimes they win, and sometimes they lose (hard to prove harm if you bought a house near an existing airport...). Over the years, we've made jets quieter, we've restricted the operating hours, and we've limited flight to sub-sonic over land. People fight over industrial plant emissions, sewer plant location, and yes - fracking locations - all the time.
I guess what I'm trying to say is that drone use will be regulated through the democratic process and not (solely) by some quaint notion of property rights.