> Yeah, I mean, if an airstrike can beat a Transformer, even a bad one, then... The Transformers aren't really a threat to the world.
> 
> Sure, the Transformers may be awesome, but if you can hurt one with an airstrike, then modern military forces will start sending hundreds upon hundreds of aircraft to whack you in the face if you start making a real bid for world domination.

Well ... it was explained, and does make sense for Scorponok. The Warthogs hardly do anything to him, while the Gunship injures him quite a bit (still doesn't kill him enough to make escape impossible). Scorponok is one of the smaller Decepticons. Plus, they didn't yet figure out what weapons were dangerous to them or not, and so the gunship actually hurting him was quite a surprise. Basically he wasn't prepared and was caught off guard. If he knew, he likely would have won. But I think Scorponok isn't too good at seeing the big picture. He is a scorpion (not quite sure if he's sentient or not)

Another issue is their ego. The transformers (especially the Decepticons) think they're superior to humans in every way. So when it happens that there's something that can hurt them, they're quite surprised because they weren't expecting it.