I think that its because, of the Mane Six, Fluttershy was the one most likely to actually befriend him. The othersdidn't even give reforming him a real chance. Twilight went to go find a spell, and when that didn't work, she and everyone else were pretty much "Turn him to stone!!"
Fluttershy tried from the beginning to be his friend, to show him just what being friends was all about, so that when she told him they weren't friends anymore, it really hurt him. He saw the error of his ways (mostly) and turned good.