James Taranto makes a key distinction. (The bolding replaces italics in the original):

We aren't at war with Islam, and declaring war on a religion whose adherents number about one-fifth of the world's population would be boneheaded in the extreme. (Ralph Peters eloquently answers anti-Muslim bigots in today's New York Post.)

At the same time, there is a reason that the illegal combatants at Guantanamo are provided with Korans and arrows pointing to Mecca rather than with Bibles or tzitzit. Islam is not our enemy, but our enemies are Muslim; and Islam as they understand it is the ideology that drives them to make war on us.

Indulge us in a little experiment: Try not to think of a giraffe. Didn't work, did it? Likewise, strained efforts to avoid characterizing the enemy as Muslim only reinforce the misconception that our war is against Islam.

Before the Gonzales meeting, we attended a Hudson Institute lunch for former Israeli prime minister Benjamin Netanyahu (the New York Sun was there as well), who put the matter very clearly. The enemy, he said, is "militant Islam," which is at war not only with Christians and Jews but with other Muslims whom the militants deem insufficiently pious.

In Netanyahu's formulation, then, the civilized world, including much of the Muslim world, is defending itself against an aggressor that is Muslim but does not represent all Muslims. And as he noted, although we are not waging a religious war, the enemy is.

Whereas the Israelis have been engaged with this problem for decades, we Americans were not nearly so focused on it until half a decade ago. Thus it isn't surprising that leaders in Jerusalem would have a more sophisticated outlook than their counterparts in Washington. But the latter clearly could stand to learn from the former.