Why would you want to wear shorts on a flight in the first place? It is cold on board, and long pants (comfy ones, though) are much to be preferred.

The original poster asked if it is considered poor manners to wear shorts on board. Answer is: In the Middle East for sure! There are local women in the Middle East who would not even travel with you in the same elevator. Now go figure what they would say if they are close to a man with shirts and shorts. Showing too much naked skin is something which a respectful person would not do in public in most of the Middle East (GCC at least).

Would I personally object? Not really. Do I find it good manners? Certainly not in the Middle East, and elsewhere in the world neither. And, finally, it also depends a little on your body figure: Sometimes it really grosses me out if I need to sit next to a fat guy in shorts with hairy legs.