In the wake of the 9/11 attacks, the Department of the Treasury belatedly woke up to the fact that a number of Islamist terror groups have been using the United States as a base from which to raise money for their activities abroad. The result was that organizations like the Holy Land Foundation, a Hamas front group, were eventually shut down. In some cases, those running these so-called charities were prosecuted.

But not everybody is happy with this outcome. The American Civil Liberties Union has just issued a report contending that the federal government’s efforts to stem the flow of funds to terror groups violate the civil rights of American Muslims. The report describes the Treasury’s actions as impinging on the religious freedom of Muslims who have a religious obligation to give to charity. The upshot, according to the ACLU and a New York Times article on their report, is that the government crackdown has a chilling effect on all Muslim charities and impeded the ability of American Muslims to give zakat – one of the five pillars of their religion.

This is a view that was seemingly echoed by President Obama in his Cairo speech to the Muslim world. He apologized for the fact that “rules on charitable giving have made it harder for Muslim to fulfill their religious obligation. That is why I am committed to working with American Muslims to ensure that they can fulfill zakat.”

What exactly the president will do to act on this promise is unclear but there are a few major problems with this conclusion.

The first is the willingness of both the ACLU and the Times to accept that giving to groups that funnel money to terrorist organizations is a reasonable definition of charitable activity. Though terrorism is the word that dare not be spoken aloud by both the president and everybody else in his administration these days, it is at the heart of this issue. In some cases, the money raised here by Islamist groups was going to needy people — the families of Palestinian suicide bombers. American money was being used to fulfill the promise that terror groups made to murderers. Other funds went to pay for the social services those groups, like Hamas and Hezbollah, provide for the poor in order to bolster their reputation and support among the population. The purpose was essentially to fund the budget of a terror group. While not every donor to such a group was completely aware of this fact, those who solicited the funds certainly were.

Second, as the Times reports, the downturn in Islamic giving has not affected all groups.

Paradoxically, two of the largest mainstream Arab-American charities — Access and Islamic Relief USA — say they have benefited from aggressive enforcement of antiterrorism laws. Islamic Relief USA, an aid organization with affiliates around the globe, has seen annual donations rise to about $25 million last year from roughly $7 million at the time of the Sept. 11 attacks, with an additional $50 million in in-kind gifts, said the group’s spokesman, Mostafa Mahboob.

In other words, those groups with no ties to terror have been unaffected by the crackdown and have prospered.

But while legitimate Muslim charities have benefited from enforcement of the laws, many of the groups that pose as the leaders of American Muslims are still tied to the pro-terror agenda of institutions like the Holy Land Foundation. For example, the Council on American Islamic Relations (CAIR) continues to be put forward in the media as a legitimate representative of Muslim opinion despite the fact that the Holy Land prosecution revealed CAIR to have been founded as a Hamas front. Moderate anti-terror Muslims are still being crowded out of the public square while those who continue to rationalize the actions of groups like Hamas and Hezbollah are treated as respectable players. If this trend is reinforced by the president it will be a setback for both America’s anti-terror actions and the efforts of genuinely moderate American Muslims who hope to break free of groups like CAIR and their terrorist partners.