You can never fly over a neutral that has never been attacked. (Note that if a power takes control of a neutral, it is no longer neutral)
You can attack a strict neutral and then fly off in a different direction in that non-com move, effectively flying over it.
Example: You can attack Afghanistan for the first time with units that include fighters from Moscow, and those fighters can then continue on to India in non-com. Once Afghanistan has been attacked by anything at all, air from both sides may freely fly over it for the rest of the game. However, other strict neutrals that have not been attacked, say Spain for instance, are still neutral and no one on either side may fly over.
Players really have to keep track of which strict neutrals have been attacked and which have not, for flyover purposes (and landing purposes). The TripleA engine does not take this into account - does not track it for you. Players could use the game notes function to track it.