First of all, I agree that the pastor is using bad judgment. However, he has a right to use bad judgment, because he's an American and we have the liberty to act stupid if we so choose.
Secondly, the BIG difference between a pastor burning the Quran and the mosque building is that while people are raising a FUSS about a mosque being built at ground zero, no one is threatening to kill large numbers of muslims because of it.
On the flip side, a pastor threatens to burn a sacred book and suddenly our troops are placed in grave danger, among other things.
Christians making a fuss about something is not the same as extremist muslims making a fuss about something because the former stops with verbal abuse and acid pens, while the latter doesn't stop until people are dead.
If folks can burn flags and Bibles in this country, then they can most certainly have a Quran bonfire and call it a "right."
So on a personal level, I don't support the pastor's actions, but from a political standpoint--he can burn books if he wants to.