I would say that Fluttershy is shy for the reason that I feel she wants to be accepted by other ponies so badly, she is afraid to make any mistakes around anyone. It is the reason I am shy as well, and in my head, it works for her as well.
Fluttershy is shy because as a filly she was mentally harassed by her fellow students due to her lack of flight skills. She contantly has a sense that she is inferior in any activities with other ponies now since they have the intelligence to judge her with whatever she does. She doesn't want to risk humiliating herself so she tries to keep to herself most of the time.
From a shy Brony (me) talking about a shy pony, I think Flutter had the same past as me: was an introvert, possible past of being bullied, fear of criticism or rejection, low self-esteem, is self-conscious, and the comfort from animals who don't judge or hate. Fluttershy is my third favorite pony (after Dash and Pinkie), but has the most in common with me.
Cause the creator made her that way? No, but im really really shy too in RL.. But.. I think she pwnd me in that
She balances the others out. The mane 6 kind of complete each other in a way. Their good points complement eachothers good points, and the not so good points, or weak spots, balance the others weak spots. For example, Rarity can be somewhat self centr,ered sometimes, and the other ponies balance that. Twi can be over-responsible so one of the ponies that balances that out for her is Rainbow Dash.. If that makes sense lol
Some theories suggest that Fluttershy is actually a world-wanted mass-murderer in Equestria, but due to her shyness and a mental disorder, no one suspects her, and after she threatens to kill or kills ponies, her disorder automatically blocks the memory of her doing so. Not really answering the question of why she is shy, but she could just not have the disorder and pretend to be shy. It's the quiet ones you have to watch out for!
It's no coincidence that I'm attracted to shy girls and Fluttershy is my favourite pony. I think she is shy for a lot of the same reasons I am, fear of being judged and ostracised. She finds it's better to stay quiet then speak and be confirmed a fool.
