In my opinion, the two reasons most people have are because it is:
Flygon is a Pokémon thats liked by many people for its design. Its also (usually) especially by fans of Hoenn. Since a lot of players have Flygon as one of their favourite Pokémon, they would want it to get a Mega Evolution.
Outclassed/In Need Of A Boost
Often outclassed by other dragons (especially Garchomp), many people who like Flygon are wishing for it to get a boost. A Mega Evolution is a great way for it to get this boost, since it has potential to be really good in competitive.
These are the main reasons why many people want Pokémon like Flygon and Milotic to get a Mega Evolution. Many people think it "deserves" a mega, because fans like it, it has potential or both. Although less common, I've also seen people who really want Pokémon like Flygon and Haxorus to get the Dragon/Bug typing.
Hope I helped!