Okay, so I came up with a theory for the Wonderbolts (obviously, by the title), so, read on and tell me whatcha think:
In the beginning, back in the old days, the Wonderbolts were a team of Equestria's best flyers that worked for Celestia. They were the main ones to clear the clouds and control the weather rather than the other Cloudsdale Pegasi, but if the Wonderbolts couldn't do it, the Pegasi were supposed to.
Despite the Wonderbolts only controlling the weather, the Pegasi still made it, needing water to be sent to Cloudsdale by a Pegasi-driven tornado. Of course, the Wonderbolts regularly had that taken care of. They were also the ones to fight off any ponies or other creatures that were attacking or threatening anything or anypony.
As a filly, Spitfire, the current leader of the Wonderbolts, was actually a pretty weak flyer, much like Scootaloo is or Fluttershy was as a filly. She was regularly picked on by other foals and Pegasi for being unable to fly, and like Rainbow Dash,