I just found this chart and i wonder if more people have interesting theories on why this shipping is working so well.

4211009
They have screentime together.

Also, she was the one who reformed him.

The Beauty and the Beast effect!
And because Fluttershy is the second most caotic member of the mane6. She always breaks the Order of Nature! ( The weak must die. )

As an incredibly shy pony, Fluttershy rarely stands up for what she believes. Many of the few and far between occurrances where she defends her opinion are with Discord. She has faith in him and sees how potentially amazing he could be - and she admires that. She also feels the wonderful responsibility of guiding him on the road of good.
This also makes Discord appreciate her kindness more. He has a confident influence on her while she has a positive and helpful influence on him. She is his first and only friend(up until season four) which makes him trust her and vice versa and naturally promoting her to 'best friend.' He feels appreciated when around her.
Both can repair the other's disadvantages/faults and understand one another. They feel like they're worth a lot to each other and self-worth is often incredibly benefiting to your happiness and attitude. They fit together like the yin and yang.

Aw man, there's soooo many reasons why this ship works so well. Especially for this show. Many of those reasons include the opposites attract dynamic done right, the chaos/butterfly theory, beauty and the beast dynamic(teaching kids that you should like someone for who they are and not their looks), great and unique chemistry, but also the fact that Discord and Fluttershy still stay who they are despite having their relationship. Yes Discord and Fluttershy help with each others flaws and create new strengths in each other, but their relationship shows us that people can still be they're true selves and not change dramatically in terms of personality for a relationship. Fluttershy is still Fluttershy and Discord is still Discord. Plus, their relationship has potential beautiful friendship turning into romance. And most modern romances and strong romances start from friendship. Which can be a great lesson for the show to tackle and keep it in tone with MLP overall. In a way, their relationship embodies what this show us all about. Any pony can be friends with anybody and the friendship can still work. Look at the Mane 6! They're all different, but they appreciate each others qualities and create an everlasting bond. Fluttershy appreciates Discord's chaos and Discord appreciates Fluttershy's kindness, and they created a bond through that.

4211009 I love the mention of how the Butterfly Effect and Chaos Theory are associated with one another. Of course, the Butterfly Effect doesn't really work with Fluttershy, but just how those terms match them makes me laugh.

To be quite honest, I am terrible at explaining why I like these two together (friendship or romance). Simply because my transition from being neutral of them took such a sudden turn into "Please get together, you're both so precious oh god what's happened to me?!" in the middle of "Twilight's Kingdom" that I have no idea why I like it so much.

If you think about it, they really haven't spent all that much time together. We have "Keep Calm and Flutter On," a little bit in both "Princess Twilight Sparkle" and "Three's a Crowd," and "Twilight's Kingdom." I'm dying more so to see them interacting more often next season than really seeing any sort of romantic relationship. I supposed compared to the others--minus him and Twilight--that's the most he's really interacted with anyone. I just really want to see them all together more often in season five!

But I do love that they appreciate their friendship so much. They write letters, have picnics, even though we haven't seen them yet. It's a cute touch, enough storytelling to tell us "Even if he's not around much, they're still good friends." Yes, he betrayed them, but he thought of her before making the final decision. She was in his thoughts, albeit just before he would break her heart. He apologized first to her when he realized, "I f*cked up." Remember that it was just a task for Fluttershy to reform Discord from Celestia at the start, and they could've just stopped there. But no; here they are, truly dealing with some heartbreaking conflict. And the emotions are real. Being back stabbed is no fun, after all. I still get upset watching this episode (just watched it again last week; me and my friend just couldn't handle it). I so incredibly love this, of all things. The conflict felt real, because they do matter to one another. And that's what gets me as a shipper; that they care about each other.

Small edit: There are arguments that go around which rather upsets me. That having them go into a committed relationship would ruin their friendship. No, no, that's the exact opposite. That's not what romance is! As someone who doesn't really plan on having a committed relationship anytime soon, I still appreciate the happiness that comes with romance. If they are the great friends they are, I don't think that would change because you can still be friends with your special one. When I dated my best friend last year, nothing really changed (minus cheesy nicknames and all that), and even though we broke up, we're still friends. Nothing changed. There are those that do change, whether good or bad, but I can sort of imagine the show going into a pair of characters getting into a more intimate relationship and how it would/wouldn't change.

And then you forget these are fictional, characters of a young family cartoon and realize you're gushing so hard it's embarrassing. *... melts into a puddle*

4212514
Yeah i noticed that there isn't many pairings in that show who show so many kinds of emotions to eachother. Discord made her scared, happy, proud, angry, sad, made her jump into his arms and cry in the same episode. i can't really remeber anyone doing this much interactions with her. Dash and Pinkie combined could possibly gain similar level. I think that this variety of emotions is also what contribute to this pairing.

4212514 Twilight's Kingdom is what got me, too! For many it's Keep Calm and Flutter On or Bride of Discord or something, but for me it was Twilight's Kingdom! Glad I'm not the only one who was effected in that way! Before then, I just thought they should just be friends, but then I watched the finale and I'm like "GOT ROOM ON THIS SHIP FOR ONE MORE????"

4213784 Haha, awesome! I'm sure we're not the only one (more love for da ship), because that dilemma certainly opened a little more interpretation than before. While watching the episode for the first time, it was like I shipped them beforehand, fangirling over it like a psycho. And now look where we are

I read Bride of Discord...

More? Well Fluttershy is patient and can live with his insanity, Discord truly cares about her clearly demonstrated by waiting til she was out of town to pull his blue sickness trick.
Honestly I still prefer shipping Discord with Luna though.