Everypony has a temperament that is relatively stable throughout life. She developed a shy temperament.
An overwhelming sense of inferiority and being judged. that's why she turns to her animals, who do not judge her because they depend on her, which gives her a sense of belonging which she was unable to feel during her time on Cloudsdale. Alright, not really. It's because it makes her adorable! :3
I assume that she was always a shy person. Even in her flashbacks, she was incredibly shy. She also has a fear of public humilation, so that doesn't help her confidence. I assume that it's because she was one of the weaker flyers in Cloudsdale, so she must've felt shy because of that. And her personality has just stuck. Also what Rarit E said.
Think about it. Pound Cake is very strong, Rarity has an interest in gems and stuff, the whole Apple family works with apples, Rainbow Dash is fast, Fluttershy is shy. It may actually be true.
Also Colgate (in fandom) is always wanting clean teeth, Berry Punch (not canon(?)) is a drinker, the Oranges are centered around oranges, Lyra has a lyre cutiemark, and there's so many others with personalities related to their names. As for Fluttershy, I think she is shy because of the events that occurred during flight school
My theory, which is similar to what Enalis said, is that all the years of bullying during flight school really got to her. Not only did she start thinking everypony was against her, but she became incredibly self conscious. Unfortunately we can't get into a nature vs. nurture argument, as we haven't seen her parents at all. They could have had a part in it as well. For example, if they are really shy, then she would have grown up with that and taken on the same attitude. They also could have instilled the fear of dragons in Fluttershy, as we don't know the history behind her fear of dragons.
I'm going with what Lightning Mustang said. One doesn't just happen to be shy, there's usually a reason behind it. One of the possible reasons is how she was made fun of during flight school may have made her the way she is. However, during the flashback we saw, she was still rather shy, so the question is begged: What made her that way previously? There really isn't enough information to speculate the cause of this; we don't know her parents, or anything else about her past really besides the fact that she's always retained a fear of dragons, but the thing that I'm wondering is if her fear is linked to it somehow, but no quality possibilities arise. One could argue that she's just shy because it's in her nature, but that's already been disproved in the same episode. Upon plummeting to the earth below she discovered a new world around her and instead of slowly taking it in, she immediately immersed herself in it; very uncharacteristic of one who is 'naturally shy'. This suggests that her shyness is stemmed from self consciousness (as stated before) of what ponies think of her, but other animals' opinions of her seem to not phase her in the slightest. Again, this begs the question of what could have made her so shy in the first place? Regardless, she's likely shy to fill the quota her name provides as Rarit E said, and we're obviously going way too deep into this than needed. In this fandom, we over-analyze cartoons.
actually, I wanted to write something like this. In flsh back, we saw that she was bullied in flight camp before, Rainbow Dash stood up for her. There's strong possibility that she was bullied before rainbow dash even knew for her, or ever saw her getting bullied.
I'm kinda shy, and my reason is that I'm afraid to say or do something stupid and to get hurt. Most people i know (who are shy) have the same reason as myself. So I guess Fluttershy also has the same ''problem'', or whatver you want to call it. Or it could just be her name, as Rarit E said.
Rainbow Dash was made fun when she was younger (Rainbow Crash...) but she isn't shy. Some people are more prone to shy behavior than others. However, in the young flier competiton, RBD broke down before it was her turn to go because she feared she would mess up. Things that make people nervous or self-conscious will affect most people, but they handle it differently. RBD has the same issue, but she hides her fear, fluttershy does not, she runs away from it. Ponies (and people) have different personalities and react to stress situations differently. Most (if not all) perceive the stressful situation the same way, it affects them mostly the same way. How they react to it depends on their personality. And personalities are formed by certain birth traits (ex. a suspicous vs a trusting trait) in combination with the what they experience in life and how they and others react to it. If running away works the first time, they'll run away every time. And her name is not "shy" it's Fluttershy. She's afraid of flying. Because if being a bad flier and having the fear of being inadequate in midair and possibly falling to your death isn't enough to make one petrified of flying, then being constantly made fun of for it will. Not only do the animals not judge her, but she doesn't have to fly in order to interact with them. Why exactly is Fluttershy so shy? How exactly is a rainbow made? How exactly does the sun set? How exactly does a positrack rear end on a Plymouth work? It just does.
