If you were to protest the Iranian regime, you should use a flag of the current regime. Burning Quran to protest one specific Muslim country is like burning Torah to protest Israel. The symbol is specific to the entire religion and not some country or administration or so. So it is always an attack on the religion as a whole.
Also Islam and (afaik) Judaism don't have a central religious authority like the catholic church does. So attacking the religion to criticize a certain institution works even less.
Also what started with burning books went to burning humans in short time.