I have the belief that flying for pegasus is kinda of like learning to walk like it is for a human. Some pegasus learn to fly faster than others and some pegsuses are more coordinated at flying than others, just like some humans have better hand eye coordination than others.
My other theory which in retrospect is kinda of wonky is that peagsus are born with some innate instinct to fly, Scootaloo may not be able to really get off the ground, but she does use her wings when doing scooter tricks, and she instinctively moves them and tries to hover off the ground. From the episode we see the flashback of Rainbowdash and Fluttershy at flying school it can be assumed two or three things happen when pegasus reach the time to go to flight school. Also it could be very young pegasus babies are more capable at staying air borne longer because they do weigh less and aren't as conscious of implications of being high up, like older peagsus are. Same way when we are younger and learning to walk and move we aren't as conscious of the consequenses failure to do those things have (a toddler walking, versus an older child learning to swim or ride a bike)
1) Some of the pegasus fillies already live in Cloudsdale
2) Another pegasus flew them there, just like Rainbowdash carried Scootaloo in the newest episode
3) We know there are means of mass transport in Equestria, there is a train and we have seen a hot air balloon before as well, so when a pegasus filly reaches the appropriate age to to go flight school there is a means of mass transport for the fillies that don't live in Cloudsdale.