Has someone ever though about how sad and difficult was Fluttershy’s life as a child?
Before getting her cutie mark, and before becoming Rainbow Dash’s friend.
She was alone, she didn’t had anyone to hug her, or talk to her.
Think about it, a child’s self-esteem is very fragile, and Fluttershy couldn’t rely on anyone. She probably started to think that it was true, and not begin good at flying made her worthless, and led it grow inside her until she BELIEVED it was true.