Umm, you seem to have a strange view of 'property'. Property has nothing to do with soil.
And if 'air rights' are different from 'property rights', then where does it start and stop? 1 foot off the ground? 5 ft? 6 ft? 8 ft? 10 ft? 20 ft? 100 ft? 1000ft?
You see the problem here, you can't really stop. And it's no more reasonable to say this guy had the right to shoot at someone for putting in a sewer pipe (below ground) then he does to shoot at a plane flying overhead.
Nonsense. Digging up and destroying or upsetting the earth is not the same as an airplane passing overhead.