It's also important to note that not many of the flying creatures in Mage Wars are flying AND have a ranged attack. If a flying creature uses a melee attack, they are "grounded" for the remainder of that round. Whenever I play my Beast Master, I take full advantage of this - willing to sacrifice the loss of a few of my weaker creatures at the expense of taking out the opponent's flying creatures should they attack.
Obviously, this doesn't solve the issue with Ruginn, The Raven Familiar (think that's his name, don't have the card in front of me), but it does help battle quite a few of the more ornery creatures like the Priestess's angels.
That being said, it obviously is worth while to make room for Maim Wings, Geyser, Jet Stream, Knockdown, Tanglevine, etc. Sometimes I've even put a banish in my deck to make sure to just get rid of a troublesome flying creature so I can focus down my opponent's mage.