The Flak Gun is very deadly to all air units due to it's great range, especially to Helicopters. It is the only turret that strictly targets air. Thus, its greatest weakness is ground units.
It can heavily damage Thunderbolts and Raptors flying directly to it only if it's not baited, but it doesn't stop a full group of Reapers quickly as they fly in circles, making it hard to deal with. It also has the fastest turn rate of any turret in the game, but AOE damage can be avoided if the player is quick enough.