Peter Bergen and Paul Cruickshank make this point in The New Republic:

After September 11, there was considerable fear in the West that we were headed for a clash of civilizations with the Muslim world led by bin Laden, who would entice masses of young Muslims into his jihadist movement. But the religious leaders and former militants who are now critiquing Al Qaeda's terrorist campaign--both in the Middle East and in Muslim enclaves in the West-- make that less likely. The potential repercussions for Al Qaeda cannot be underestimated because, unlike most mainstream Muslim leaders, Al Qaeda's new critics have the jihadist credentials to make their criticisms bite. "The starting point has to be that jihad is legitimate, otherwise no one will listen, " says Benotman, who sees the Iraqi insurgency as a legitimate jihad. "The reaction [to my criticism of Al Qaeda] has been beyond imagination. It has made the radicals very angry. They are very shaky about it."

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.

Zawahiri has watched Al Qaeda’s popularity decline in places where it formerly enjoyed great support. In Pakistan, where hundreds have been killed recently by Al Qaeda suicide bombers—including, perhaps, former Prime Minister Benazir Bhutto—public opinion has turned against bin Laden and his companions. An Algerian terror organization, the Salafist Group for Preaching and Combat, formally affiliated itself with Al Qaeda in September, 2006, and began a series of suicide bombings that have alienated the Algerian people, long weary of the horrors that Islamist radicals have inflicted on their country. Even members of Al Qaeda admit that their cause has been harmed by indiscriminate violence. In February of this year, Abu Turab al-Jazairi, an Al Qaeda commander in northern Iraq, whose nom de guerre suggests that he is Algerian, gave an interview to Al Arab, a Qatari daily. “The attacks in Algeria sparked animated debate here in Iraq,” he said. “By God, had they told me they were planning to harm the Algerian President and his family, I would say, ‘Blessings be upon them!’ But explosions in the street, blood knee-deep, the killing of soldiers whose wages are not even enough for them to eat at third-rate restaurants . . . and calling this jihad? By God, it’s sheer idiocy!” Abu Turab admitted that he and his colleagues were suffering a similar public-relations problem in Iraq, because “Al Qaeda has been infiltrated by people who have harmed its reputation.” He said that only about a third of the nine thousand fighters who call themselves members of Al Qaeda in Mesopotamia can be relied upon. “The rest are unreliable, since they keep harming the good name of Al Qaeda.” He concludes, “Our position is very difficult.”

In Saudi Arabia, where the government has been trying to tame its radical clerics, Sheikh Abdul Aziz bin Abdullah Aal al-Sheikh, the Grand Mufti, issued a fatwa in October, 2007, forbidding Saudi youth to join the jihad outside the country. Two months later, Saudi authorities arrested members of a suspected Al Qaeda cell who allegedly planned to assassinate the Grand Mufti. That same fall, Sheikh Salman al-Oadah, a cleric whom bin Laden has praised in the past, appeared on an Arabic television network and read an open letter to the Al Qaeda leader. He asked, “Brother Osama, how much blood has been spilled? How many innocent children, women, and old people have been killed, maimed, and expelled from their homes in the name of Al Qaeda?” These critiques echoed some of the concerns of the Palestinian cleric Sheikh Abu Muhammad al-Maqdisi, who is considered by some to be the most influential jihadi theorist. In 2004, Maqdisi, then in a Jordanian prison, castigated his former protégé Abu Musab al-Zarqawi, the now dead leader of Al Qaeda in Iraq, for his unproductive violence, particularly the wholesale slaughter of Shiites and the use of suicide bombers. “Mujahideen should refrain from acts that target civilians, churches, or other places of worship, including Shiite sites,” Maqdisi wrote. “The hands of the jihad warriors must remain clean.”

Today, al Qaeda [in Iraq] has been shattered, with most of its leadership and foot soldiers dead, captured or moved from Iraq. As a result, al Qaeda attacks have declined more than 90 percent. Worse, most of their Iraqi Sunni Arab allies have turned on them, or simply quit. This "betrayal" is handled carefully on the terrorist web sites, for it is seen as both shameful, and perhaps recoverable.

Maybe this will be history's judgment of the last few years: both the US and al Qaeda over-reached. But al Qaeda's over-reach was greater. And in this we see why democracies do actually do better in warfare in the long run: because our leaders have to be responsive to the people; because legitimate internal criticism and debate forces course correction and exposes self-defeating hubris. With the Bush administration, this process took much longer than it should have, and the Bushies did all they could to stamp out, rather than hear, criticism. But in the end, democracy adjusts to reality; religious extremism cannot.