Any air combat hits are most likely taken against incoming bombers and from our games there are is usually only one or two bombers in a raid. If one protects important territories with perhaps 3 fighters then that should take care of one bomber. Any tanks or artillery will also get AAA.
Losing rail or a factory space or a resource is not that devastating overall. Losing a stack of units under construction is painful and thus one has to consider where to build and how much to protect.
Do not see an issue yet with strategic bombing or surface bombing. Bombers are costly and vulnerable (i.e. fist hit).