Yes, there will be flying in Legion. After the 6.2.2 WoW patch, we finally have flying in Warlords of Draenor (after completing certain conditions, though most people will have already met them). The same template for achieving flight will probably be used in the upcoming expansion – but not right away.
Blizzard have been pretty vague on the specifics regarding Flying in Legion, but the company seems to be suggesting that flight will be unlocked via an achievement rather than by paying with gold. This could take the form of a quest, finding a certain item, exploring areas or possibly from requirements such as rep. As with Draenor, Blizzard have said flight won’t be immediately available. All this may change, of course, as Blizzard likes to constantly remind people that statements aren’t promises.