What Most of the answers will be
Because Chickens can't fly and you can't teach a dictionary magic

What my answer will be
Money is the likely answer, the Magic school is in Canterlot, and the Flight school is in Cloudsdale both cost a lot of bits to go to

My guess is this will somehow fit into the CMC’s story. Here’s how I see it going down:

All three will be away from each other. Sweetie Belle at some magic school and Scoot at some flight school and Apple Bloom stays home. (Each will get a few episodes on their own) Then they all end up getting their cutie marks when their separated. Then when they meet back up each hids the fact they got their cutie mark so other others don’t feel left out/jealous, despite the fact they all have theirs now. Then shenanigans; as each tries to keep their “secret.” Finaly they all find out and feel awful silly. Cue Twilight/Spike and friendship report.