It's a mix of not allowing people to blitz through everything, and allowing them to design better world content when they can have a reasonable idea on how players will tackle it. Sadly most of these happened during leveling in WoD so it didn't give no flying any real credit at max level. Flying changes the dynamics between player and environment so much it has way more ramifications than just being a question of travel speed. You'd have to be pretty blind not to notice that more and more world content has to be designed in local indoor areas (towers, bunkers, fortresses etc) to stop players from just swooping down at the end.
If no flight is purely for slowing down people's progress, then there's a billion other ways to accomplish that. And such systems ARE in play already. Who decided the price of artifact traits? Amount of exp to level? Amount of mats to craft the best profession gear? Droprates? Quest objectives? How fast we get reputation? Base movement speed? Gear requirements in raids etc?
All of these are "slowing us down"... because this is not a sandbox. This is a progression-based MMOs and those generally don't spoonfeed everyone the moment they log in and hand out gold stars and loot for participation only.
It's ALL a part of pacing the game and how we progress. Stop making it sound like a money grubbing scheme because it isn't. If staggered flight is a way to prolong content / increase subs, then EVERYTHING is.