When I fly in an aircraft, I look for lone guys in good perches with my infrared. It's painfully easy to find them at certain ranges, and then they are hosed. I imagine you are encountering this. 50 certs on pods and your hiding place is now a golden thrown screaming "100xp here!" When I go as an infiltrator, I try to make sure I have overhead cover as well from a bit of building, a tree, or like my friend did the other day: he sat next to me in an skyguard lightning. Didn't get molested by aircraft during the entire battle.