* Flying is limited: The ability to fly is unlocked late in the game, and only allows travel to cities you've already visited. Mossdeep City is your next destination on the main storyline, so you haven't been there yet.
* Traveling to Mossdeep: You'll need to travel to Mossdeep City by land. The most direct route involves following the eastern coast of Hoenn, heading north past Slateport City.
Enjoy your journey!