The command /fly was not made by Mojang and instead made by 3rd party developers so technically they did not make it and servers can profit off it. Also, there are fair and reasonable ways to achieve flight. BUT if you were on a game mode such as factions where it can be considered Pay 2 Win if there are not legitimate ways to achieve it could possibly be considered against the EULA. If I have made any mistakes feel free to correct me as its been a year or so since I have read the EULA.