I'm having issues figuring out how to get my level 90 to fly instead of use the ground mount. I was wondering if this was possible and if I needed to edit something in the profile to make it work?
Profiles are either written to Fly on selective 'hops' while executing the profile, or just use the ground mount. Once a profile is cast in such a manner, it is unreasonably time consuming to go back and 'reflow' it. Also, since questing profiles are designed for leveling, and not in general "run by level 90s", then it is actually undesirable to do this, anyway.
Wait for Native flying to come out of Beta and be released to the Community
Reflowing a profile to fly is not a solution that is going to happen. Too much time and testing involved to do so--especially with "native flying" on the way.