Flyers are counter-able. Have your own Flyers to intercept and shoot down the enemy Flyers. Seriously, take some Flyers and wreak havoc on your foes like they have been doing to you. Or take an allied Squat force, consisting of Overlord Airships. Those can shoot at Flyers with impunity. You have options. If you don't like the existing options, use the Points Formula and build some new ones.