(Sorry, I just noticed your thread in "General Discussion" and moved it here to the "Help" category.)
Air units take damage when flying over enemy units (land and sea) and defense turrets. From GT's Help section:
"The path from the air base to the target is important because the units will take fire from any enemy units or defense turrets they fly over during their attack. Land units fire at 10% strength, sea units at 40%, and defense turrets at 100%. (Units/defenses owned by countries with which you have a treaty will not fire on your units.)"