Because...
Well, duh...
Lopunny runs Physical Sets (you've ever seen a SPECIAL attacking Lopunny?), and since it has soooooooo much speed, you need a nature to help it speed out Adamant EV trained 252 Speed Lopunnys (or something like that).
But why not a Adamant Nature, when it has a boost for attack?
Because then you would have no advantage of its DEADLY speed, and then you might get KOed by something (if not careful). But still, no advantage what so ever.
So that's why those 88.9% of use Jolly, to take advantage of its rediculously fast speed.
EDIT: Since I found out it couldn't learn Swords Dance by TM, I decided that Power-Up Punch could help it maximize it's attack.
Here's a movesets for competitive:
Lopunny@Lopunnite (or it's Mega Stone name (can't spell it >.>))
Jolly Nature
EVs: 252 attack / 252 Speed
Ability: Cute Charm -> Scrappy
- Power-Up Punch (To maximize its attack)
- High Jump Kick/Protect (whichever you want)
- Return (Maximized when Mega Evolved)
- Toxic (filler move, to cripple if not...)/ Substitute (take some pain, take no damage)/Baton Pass (Maximized Attack = Deadly Attacker on the next turn)