Flying units may move great distances and may cross enemy lands without restrictions. Seas cannot be crossed by flying and still requires a full move to enter or exit. Fliers are also able to launch quick attacks on archers and commanders in battles. Flying units are very good at patrolling your lands. They are also difficult to besiege and will have an advantage when besieging others.
Note: When using flying units in combat, consider having them hold and attack rear rather than simply attack rear, lest nearby units that would otherwise be too far and going for your frontline switch target to your fliers.