Of course flying mounts are going to be better, especially right now when they are the new shiny. There are still times when you need to go to ARR areas though so they will still be used there (unless of course people really like a paticular flying mount), and many current ground-only mounts will be givin flying capabilities as well.

As well, even if you finish all the sidequests in an area and get flying as soon as possible, most of the areas have sidequests that open up later on in the story so you for certianly have NOT done all of them yet by the time you get flying. Atleast if you are getting it as soon as possible.