It wasn’t the burning per se that made this such an issue - burning is the proper disposal method. However, it was that it was done disrespectfully - they burned the Quran with the trash.
NPR has an interesting article:
How To Properly Dispose Of Sacred Texts
An Iman from Falls Church, Va said:

“If one said, ‘Well, we’re burning some Qurans today,’ that wouldn’t incite riots in Afghanistan,” he says. “The problem is when one puts a malicious intent as part of the burning.”

Malik says the assumption there is that Americans disrespect Muslims. That’s why there would be such a visceral response to burning the Quran, even though a layperson could do so under Muslim law — as long as the intent was respectful.

So this mess could have been avoided if someone with some forethought (considering the riots over that idiot in Flordia) would have sought the advice of a local leader or local Imam.