The ants implemented as an annoyance do their job splendidly. They are annoying, which is a fine addition to the game; however, they are annoying for the wrong reasons.
I'm sure the AI for the flying mounts have been mentioned before. In order to keep a bird from disappearing on you, you have to force them to stay put and set their aggression to "Passive." That means if something starts hitting your bird, it's going to sit still and take all the punches while you're busy mining, gathering or scouting. This causes the ants to be unduly annoying. It's not a matter of added difficulty, but mount's AI at it's current state doesn't allow your animal to defend itself. A high level bird can easily be lost to some low to medium level ants during a bathroom break, or a server restart.
For these reasons I suggest enabling flying mounts to be able to attack while landed. The current AI enables landed mounts to walk unless told to stay put. The player must whistle this command with each landing in order to keep them in a secure or designated place. If the mounts were able to attack while landed, an adequately leveled mount would be able to defend itself against an annoyance while staying in it's designated area. Poorly placed mounts would still fall victim to bigger threats such as the sabertooth, raptor, rex and so on.
Addressing the current issues with flying mounts wandering once attacked, perhaps an item or a built nest could act as a kind of home point. Tamed flying mounts left unattended after a time could eventually begin to travel back to "home."