I listen to this guy

Michael Scheuer, formerly a CIA analyst and head of the group specializing in Bin Laden, previously published two books under the pseudonym Anonymous.  I don't always agree with his prescriptions by any means.  But I take his analyses seriously.

In A Fire Bell in the Night for the West? Antiwar.com 05/19/05, he writes:

While the violence over the Koran-desecration story may or may not continue, it is important not to hastily cross off the incident as an ephemeral issue. It is even more important to avoid attributing the reaction to al-Qaeda's cynical manipulation of the crowds, or knee-jerk anti-U.S. bashing by anti-Western Muslim governments. Instead, the Newsweek article provides a timely opportunity to test the two main Western assumptions that undergird strategy for the War on Terrorism: (a) barbarism not faith motivates Islamist terrorists, Islamic militancy, and anti-U.S. Muslims, a group small in number and on the fringe of Muslim society, and (b) America and the West are hated for what they are and not for what they do.

"Fire bell in the night" was the image Thomas Jefferson used for the Compromise of 1820 and what it portended for the future of the Union.

On both issues, his reading of he situation doesn't give much comfort to the Republican Party line of the moment.  On what is behind the demonstrations and the reactions to the Qur'ān desecration reports, he writes:

[T]he intensity and extent of the popular reaction suggests that it would be incorrect to assume that only those who support Islamist leaders like Osama bin Laden viewed the episode as an attack on the Islamic faith. ...

The purported desecration also earned attacks from some of the world's most senior Islamic religious leaders. In Egypt, the Grand Mufti Dr. Ali Gomma termed the incident an "unforgivable crime" in the face of which Muslims cannot stand with "hands folded," while the sheik of al-Azhar University, Mohamed Sayed Tantawi, said, "The Quran's desecration is a great crime and should be dealt with at once." This reaction also bridged Islam's Sunni-Shia divide. The Sunni grand mufti of Lebanon, Muhammed Rashid Qabbani, for example, described the event as a "crime" and called for an investigation by a multinational committee with Muslim state members, while Lebanese Shia leader Sheik Mohamed Hussein Fadlallah called the reported desecration as "part of an American program – of contempt for Islam," and "one of the American methods of torture" used against Muslims. (my emphasis)

The al-Azhar University in Egypt is the most prestigious institution for establishment Sunni Islam, i.e., the kind the US would presumably want to encourage in preference to Islamic fundamentalism.

He also thinks that Muslims are responding to the actions of the West, not to some abstract notion of our institutions being bad, i.e., "they hate us for our freedoms."  Scheuer puts particular emphasis on the fact that the protests do not seem to be driven by the jihadists.  On the contrary:

To date, not one of the major Islamist militant leaders – bin Laden, Zarqawi, Zawahiri, Abu Bakr Bashir, et al. – has said a public word about the desecration incident, and yet worldwide demonstrations have occurred and the air has been filled with harsh condemnations from government and religious leaders.

One of Scheuer's main themes, and not only in this article, is the analytical point that in much of the Muslim world's hostility toward the West that religious faith as such is an important motivator.  Recognizing that doesn't require the US to adopt a particular strategy; it's just one part of the "reality-based" picture that needs to be recognized.  But the "they hate us for our freedoms" mantra is an excuse for overlooking that.  He writes in his conclusion:

Before attributing the Koran controversy solely to a poorly sourced magazine article and the ability of al-Qaeda and other groups to cynically exploit it, the West would do well to draw a lesson from the episode that would help formulate better plans to cope with and defeat Sunni militancy. That lesson is simply to conclude that a substantial number of the West's opponents in the War on Terrorism are motivated by faith, and that they find U.S. and Western actions – especially those that seem to target Islamic sanctities – overwhelmingly more offensive and humiliating than the norms and lifestyles of Western societies.

Michael Scheuer is definitely worth listening to carefully.  He's one of the few genuine experts on Al Qaeda, Bin Laden and the jihadist movement around in the US.