I don't think the Koran should be burned. At minimum, one should at least read it first.
That said, making the Koran a special case of 'a holy book thou shalt not burn' is precisely the state of affairs the radical Muslims are after. They are supremacists through and through. What does it say about the US, or the West in general, if we get to the point where one can burn a Bible, or fashion 'art' in the form of Piss Christ but we have to treat Islam with kid gloves? I would venture to say we look pretty cowardly.
Also, whatever Jones' shortcomings are as a Christian, he flat-out doesn't rate being put into the same category as those who would murder other people over a book they didn't even burn. He just doesn't.