But just before I do, I'd like to say that this interpretation of my fic is mine alone. And although it sounds kinda weird saying that, if people have interpreted it a different way or found a different meaning in my words, that is completely awesome and you are right too! The metaphors are very general and could apply to lots of different things. As an author, I usually don't like to say "well this is how it is", but I don't want anyone confused, so I'll try to explain as best I can.
Ok, I have a feeling this explanation is going to be long-winded, but hopefully it will clear up any confusion and give you a little more info on the Hilde of my story, 'cause to answer your question, I’ve kinda got to start from the beginning. *takes a deep breath* Here goes:
In this story, Hilde has grown considerably from the very flat character in Gundam Wing who is sadly mostly remembered as “that girl who hangs with Duo”. Because her character is not portrayed in much depth in the series, it allows me the freedom to really expand her into a complex character, building on the traits I saw in the show: determination, strength, kindess, etc.
I guess I imagine the college Hilde I portray now to be the kind of girl who is independent. Although she loves to be social, she needs her space and freedom. College often makes people very aware and appreciative of newfound independence, as I know from experience.
Although Hilde has been a support for Duo over the years, it certainly doesn’t mean she’s clingy or completely dependent. She’s a really tough chick who can hold her own, but once she’s let someone in, I see her being a total romantic at heart.
After I have Duo crushing on Relena, the Hilde in my story grows a bit wiser when it comes to relationships. To me, Duo was probably of her first true love/friend. She was very na?ve and open, and she wore her heart on her sleeve during her time with him. As a result of the abrupt break in their relationship, Hilde grew more guarded of her feelings, and learned to be more self-sufficient as well. From experience, a break-up is often both very hurtful and freeing at the same time. Without Duo, Hilde was un-attached and on her own. As she rises above the initial feelings of the loss, she begins to realize the feeling of freedom, and the safety and happiness of it. If she’s on her own, no one could touch her or hurt like she had been hurt with Duo.
Ok, with me still? Now to answer your question:
The reference to flying and wings I use simply has to do with independence, along with the safety and happiness Hilde associates with it. Flying, or being independent, is more of a mechanism for as you say, "staying out of reach from being hurt".
I played upon the common idea in many GW fan fictions that describe Hilde as a pixie, and use the image of this conveniently winged creature to further the notion that Hilde is un-attached and free of a relationship at the moment. She still has wings that enable her to fly free on her own. If someone, mainly one Trowa Barton, kept getting close to her, touching her in the deepest sense of the word, Hilde realizes that she would fall for him and enter a relationship, giving up her independence, taking the risk of being hurt, thus losing her ability to “fly”. This is why I use the similar example of a butterfly’s wings. If a person touches the wings of a butterfly too much, they will damage the thousands of tiny, delicate scales on them, and the creature will no longer be able to fly.
Ok, so on to the ending line…
Hilde basically has a revelation. She finally discovers she loves Trowa, and as the thought sinks in and she’s looking at him, she realizes that her previous musings on relationships, freedom and flying were wrong. She let herself be touched by Trowa, and instead of feeling bound or taken, her love only made her feel more happiness, more freedom. I believe this is the first time Hilde felt true love, and with Trowa, who never asked anything of her, she discovers she’s still free to be independent. (Quote: “He never asked for my love, he just…loved me.”)
And just in the course of typing this, I’ve realized where I got this idea. The concept of love as freeing, and not binding yourself to another person, comes from a wonderful book I read called The Mastery of Love, by Don Miguel Ruiz. An important lesson in it is that when people think of love, we think of needing each other; however, to love with no conditions is the true meaning of Love. This freeing experience when Hilde discovers she loves Trowa and Trowa loves her-- each one not demanding anything of the other--that is how Hilde finds she is still flying, still free. She knows she doesn’t have to be afraid of being hurt, she doesn't need to flutter (or run) away from Trowa anymore. Hilde can be on the ground with Trowa, and her heart will still be flying with freedom and happiness. Thus, “she realized that she could still fly with her feet on the ground.”
For a little extra insight, here's a quote from the book The Mastery of Love:
"Love has no expectations. Fear is full of expectations. With fear we do things because we expect that we have to, and we expect that others are going to do the same. That is why fear hurts and love doesn't. We expect something and if it doesn't happen, we feel hurt--it isn't fair. We blame others for not fufilling our expectations. When we love, we do it because we want to, and if other people do it or not, it's because they want to or not and it's nothing personal. We don't feel hurt because whatever happens is okay. That is why hardly anything hurts us when we are in love; we aren't expecting that our lover will do something, and we have no obligations." (pg. 59-60)
Ooooook. That was really, really, entirely too long. I know I probably put you to sleep or bored you to death. If I’ve confused you anymore, I’m sorry. Email me so I can try to ‘splain better or maybe I can fix it so it will make more sense.
I really appreciate you asking me questions, though, and reading through the chapters carefully. It’s really an honor to a fanfic writer when people notice the little things.
~Sphinx
I can't wait until the next update, but try not to make us wait to long. Patience is for Christmas!! 
), I love this story and your writting! Vraiment! 
But thanks to you and everyone giving me such great feedback, I was really inspired to get my butt in gear and finish the story. And thanks for your suggestions. Even though Duo and Trowa never did get into a fight, I was definitely inspired in the Epilogue to have some threats of punches because of your suggestion, because I could totally see both of them being very overprotective, so thank you! And oh, the quiet ones...I always imagine them to feel the most deeply, just as you say. You gotta watch those quiet ones. 
**sphinx says this as she's known to be one of the quiet ones** mwhahaha
I'll go before I start to scare you all too much. Thanks to everyone again for your wonderful replies! And sorry I took so long to get back to you.