(originally a comment on the Sudanese Thinker blog)
I fear that there are two problems that Islam faces because both are widespread among Islam's supposed adherents.
The one problem is a misunderstanding of where the battle is to be fought and against whom.
But the bigger problem, from the perspective of non-Muslims, is something else.
It is the pathetic ignorance displayed even by those who are wise enough to know where the battle must be fought.
The infidels do not in fact kill thousands of Muslims. In Iraq Muslim terrorists kill Muslim civilians, the Americans are barely involved. In Sudan Muslims kill Muslims in much higher numbers. In Palestine Muslims attack Jews and the Jews fight back, killing surprisingly few civilians considering where Israel's targets are located (few terrorists possess the decency to hide their bomb factories outside civilian neighbourhoods).
Muslims, those that follow what is now known as Islam rather than what I would call "orthodox" or "Quranic" Islam, tell themselves that it is not other Muslims but infidels who kill; tell themselves that Jews fighting for their survival constitutes aggression; tell themselves that terrorists bombing mosques is in fact a desperate attempt to defend Islam against the American devil. They tell themselves that and find it a handy excuse to kill non-believers, preferably Jews.
Quranic Islam does not, I think, treat Christians and Jews as "non-believers". Christians and Jews have been given, according to Quranic Islam, the prophecies and Christians and Jews believe in what they were given and the one true god. They are not unbelievers and war against them does not constitute war against infidels. It is a war against believers, a war against Allah's followers.
It is surprising, from my point of view, to see that many supposed Muslims actually believe that destroying a mosque in Iraq constitutes fighting infidels; that the destruction of Israel, in spite of Allah's plans for the land, according to the Quran, constitutes an honorable task; that ignoring the murder of hundreds of thousands of Muslims in Sudan constitutes loyalty to one's fellow Muslims; that taking control of the holy cities away from Muhammed's family constitutes a purer interpretation of the religion.
Perhaps a new word is needed to describe that form of "Islam"; those followers of a god who is not the god of the Quran, who would actually be a second god, if anything.
Perhaps a distinction should be made not between Shi'ite and Sunni but between orthodox Islam and the belief in the second god.