I'm going to go on record and say that Terry Jones is a fucking moron. He thinks that by burning Qurans, he's going to somehow convince the Iranian government to release a Christian cleric being detained (for converting to Christianity).
Now let's just throw the whole burning-sacred-texts-is-bad thing, and let's just look at this logically. Jones, a Christian, wants to convince a Muslim government to let go of an "infidel" Christian cleric. So to show them how serious he is, he burns Qurans.
Right, because torching their sacred text is really going to make them stop and think "you know, Christians really aren't that bad!"
What's more likely is that Jones was simply looking for an excuse to burn Qurans, an excuse that he probably thought would be more acceptable than "I hate Islam."