I don't think there has ever been an official explaination. During the planning for the series Lauren Faust had the idea that Scoots was handicapped and couldn't fly, but would learn her worth in other areas. But those episode ideas never happened, so it's still unknown if Scootaloo can learn to fly or not. However if you watch the series carefully, her flying ability is gradually improving and she can hover better than she used to. It may turn out she is simply a late developer.