You have a point, but remember that "Freedom of Religion" in the Constitutional sense, means that the government cannot establish an official religion.
If we have another Muslim sponsored, 911 style attack in the U.S., it won't be the government, it will be the citizens who will make sure that Islam is no longer a threat to this country.
I predict that it will take another attack on this country, the USA, and the angry backlash will be so bad that the Islamic threat will be no more.