Try guessing what having gills means for creatures that live solely on land, please. Gills are not very useful on land, creatures that have disfunctional gills on land can simply reproduce. They probably disappeared because it is a hole of protection, weakness for infections, loss of water due to evaporation.
One could ask the question why we breathe through the same hole we eat from, because of which we can choke on food. Somehow, is simply to complicated for evolution to solve the problem of redirecting the airways, while not increasing chances of infection and such. (like a hole in the chest could in principle be better for humans)