There was much to commend in President Obama’s speech at a Baltimore mosque today. The president was characteristically eloquent in denouncing religious prejudice, praising religious freedom and appealing for an inclusive society that did not judge its citizens by their faith. These are views that are neither liberal nor conservative. Nor are they nor should they be, the property of either the Democratic or Republican parties. He was also right to point out that the overwhelming majority of Muslim Americans are law-abiding citizens and should not be held personally accountable for the violent actions of other Muslims, either abroad or at home. Muslims do serve in our Armed Forces and are part of the fabric of our society and are entitled to the same rights and respect as everyone else. Muslim children should not live in fear of being singled out or of being rounded up or in any way be denied equality under the law.

Moreover, given the willingness of some Americans, including Donald Trump, to consider treating Muslims differently than other citizens, there was an argument to be made that this is exactly the right moment for a U.S. president to go to a mosque and say these things. Such sentiments are very much in keeping with President George Washington’s letter to the Jews of Newport, Rhode Island in which he memorably stated:

For happily the Government of the United States gives to bigotry no sanction, to persecution no assistance, requires only that they who live under its protection should demean themselves as good citizens, giving it on all occasions their effectual support.

But in February 2016, there is more at stake in the intersection between Islam and America than these noble sentiments. Though President Obama understands that we are living at a time when Muslim terrorists threaten the world, in his commendable desire to protect American Muslims from potential bias, he downplayed the nature of that threat and the extent of the support it gets from Muslims around the world.

American Muslims are, as the president asserts, largely the ordinary, good citizens who are no different from those that attend other houses of worship. Yet by crafting a narrative that revolves around of the notion of their being the victims of an intolerant society, he not only does this nation an injustice. He was also making it more difficult for American Muslims to condemn the terrorists and all they stand for, as he says he wishes them to do.

Even more importantly, by not directly acknowledging the popularity of radical views, even in some sectors of American Islam and especially abroad, he misrepresented the nature of a life and death conflict in which this country has found itself. By maintaining the pretense that Islamist beliefs are marginal in the Muslim world rather than a major force with a huge following that has made inroads even in American mosques, including, apparently, the one he spoke at today, he has made resolution of this conflict more difficult and, ultimately, done no favor to American Muslims.

The president acknowledged that his critics believe he has failed to lend moral clarity to the U.S. effort against ISIS terrorists. In the view of the administration, America’s foes are merely “violent extremists” rather than Islamist terrorists with little credit given to their overt Islamic identity and purpose. In his view, this is wisdom because labeling the terrorists as Islamic grants them much needed legitimacy they don’t deserve.

But while he is right to say that many Muslims oppose ISIS and that most of their victims are their co-religionists, he is wrong to say that Islam is not “at the root of the problem.”

It is all well and good for this president to assert, as his predecessor has done, that Islam is a “religion of peace.” Many Muslims believe this is so, and we should hope that their interpretation would become universally accepted. But no matter how sympathetic President Obama may be to the Islamic world, he does not have the religious authority to determine what is or is not Islamic. The problem is that ISIS, al Qaeda, Hamas, the Muslim Brotherhood, Hezbollah and even the Islamist regime in Iran are not marginal forces in the Muslim world. Islamist parties and movements have widespread support as well as the backing of major religious leaders and institutions. Though they differ on tactics and are divided by many issues, their belief that Islam is fundamentally at war with the West is not a view that is restricted to a few lunatics in the Syrian desert who are beheading people.

As it happens, the Islamic Society of Baltimore has its own connection to that world since one of its former imams, Mohammed Adam El-Sheikh, was a member of the Muslim Brotherhood in Sudan and then served on the board of a group that was cited by the Treasury Department for its ties to al-Qaeda and the Taliban while he was in Baltimore. He subsequently went on to serve at a mosque that had been led by the infamous Anwar al-Awlaki, a terrorist that was later killed in a U.S. strike.

To note these disturbing ties is not to argue that members of this mosque should be denied their rights as Americans or make them guilty of any crime. But it does show that even a mosque that has been singled out by the White House for this honor has a troubling association that illustrates the broader problem of the wide acceptance of such views. Indeed, if a Republican president were to visit a church with similar ties to radical rightists or racists, there would be a hue and cry from liberals about this being an implicit sanction for such views.

The president is right to assert that American Muslims are in a unique and important position to be advocates for both democracy and religious pluralism. But so long as their institutions find places for radicals and the groups that claim to represent them, like CAIR, are fatally compromised by their origins as front groups for terror apologists and stands that seek to rationalize terror and oppose efforts to monitor terror supporters, American Muslims won’t be able to play that important role.

The president wasn’t wrong to speak of religious freedom at a mosque. But by failing to challenge the Muslim world to confront the extent of the virus of hate and terror within it and by reinforcing the false backlash narrative, President Obama may have done more harm than good.