...
Yeah right.
Of course they didn't live happily ever after. No one can do that, unless they're on the verge of death. Fluttershy and Rainbow Dash still had problems they needed to work out, just like every other couple in all of Equestria. They aren't perfect. This world that they're living in isn't a perfect world. It has problems and challenges that ponies have to work through. That's just life.
Isn't it beautiful?