Peter Bergen and Paul Cruickshank's article is also worth a read:
Why have clerics and militants once considered allies by Al Qaeda's leaders turned against them? To a large extent, it is because Al Qaeda and its affiliates have increasingly adopted the doctrine of takfir, by which they claim the right to decide who is a "true" Muslim. Al Qaeda's Muslim critics know what results from this takfiri view: First, the radicals deem some Muslims apostates; after that, the radicals start killing them. This fatal progression happened in both Algeria and Egypt in the 1990s. It is now taking place even more dramatically in Iraq, where Al Qaeda's suicide bombers have killed more than 10,000 Iraqis, most of them targeted simply for being Shia.
Recently, Al Qaeda in Iraq has turned its fire on Sunnis who oppose its diktats, a fact not lost on the Islamic world's Sunni majority.
Additionally, Al Qaeda and its affiliates have killed thousands of Muslim civilians elsewhere since September 11: hundreds of ordinary Afghans killed every year by the Taliban, dozens of Saudis killed by terrorists since 2003, scores of Jordanians massacred at a wedding at a U.S. hotel in Amman in November 2005. Even those sympathetic to Al Qaeda have started to notice. "Excuse me Mr. Zawahiri but who is it who is killing with Your Excellency's blessing, the innocents in Baghdad, Morocco and Algeria?" one supporter asked in an online Q&A with Al Qaeda's deputy leader in April that was posted widely on jihadist websites. All this has created a dawning recognition among Muslims that the ideological virus that unleashed September 11 and the terrorist attacks in London and Madrid is the same virus now wreaking havoc in the Muslim world.