When does Son Goku learn to fly?
It was never shown, how he learned to fly, so that's pure speculation. The DragonBall-Wiki has a possible explanation:


  Goku likely learned how to fly from Kami during his long training at Kami's Lookout, as he was unable to do so before and demonstrated his abilities to conclude his World Martial Arts Tournament fight with Piccolo.


Source: Dragonball Wiki