Hussein Ibish makes the plausible case that they do speak out against terrorism, but that we have trouble hearing them:
In fact, of course, there had been a considerable outcry of condemnation around the Muslim world and particularly in the United States from the Muslim community, not only of the most recent outrage and 9/11, but of almost all the major terrorist acts in between. Yet once alleged, the question has persisted and never been resolved. The question continues to be routinely posed to Muslim-Americans: "why is your community silent about terrorism?" It has all the qualities of a trap question, in which answering invites one to accept self-defeating premises, a little like a politician being asked when he intends to stop beating his wife.
Hussein also grapples with the strongest argument made by critics of Muslim organizations and clergy, that they condemn the killing of American civilians but are more forgiving when it is Israelis who are being killed:
What has, however, troubled me for a long time and as I have continuously been complaining since at least 2004 is that while the mainstream Muslim clergy around the world has been quite good at taking a stand against terrorism generally, although not at communicating that to the non-Muslim world, there has been a most unfortunate tendency to try to make an exception for the Palestinian case on the grounds of self-defense and lack of any other options in combating occupation. Obviously, I reject any idea that combating occupation or having limited other options for armed combat can suddenly make illegitimate tactics legitimate. This point of view is, I think, less widespread than it used to be, but making moral exceptions for one's friends or certain exigent circumstances is, at best, a cynical political gesture and not a moral or religious position.