I started playing the game today, and am having some struggle understanding how to fight back at flying units. Can only archers or flying units attack them? I'm trying to figure that out thanks.

Yes, it is only archers or other flying units. I think maybe you can attack with magic as well.

Also if you give a magic bow (or crossbow?) to a unit it can then attack flying units.

One frequently given advice for newer players is to invest sufficiently in Sky Hunters for air control.