http://images3.wikia.nocookie.net/__cb20120723173145/mylittlebrony/images/2/26/Rainbow_dash_walking_by_astridautumn-d3lecv0.gif
if I may present exhibit A, please take note of the shape of a pegasi's wing
You'll notice the three large outer feathers, those are called the Primaries or Pinion feathers. Long stiff feathers that are essential to flapping flight as they are the priciple source of thrust, moving an avian up and forward through the air. As there are only three on any given pegasus, it's vital that they remain intact, this can be seen in May The Best Pet Win when our subject here is pinned by only a single feather and again in Wonderbolts Academy when a damaged Primary feather affected Rainbow's control to a noticable degree.
Scootaloo is missing one of these feathers.
It was lost during Hearts and Hooves Day when Sweetie Belle carelessly plucked it out for the purpose of making a love potion. Without this essential feather, even if flight were attained it would be lopsided and awkward, keeping Scootaloo effectively grounded.