A poster to the Caucus blog makes the key point (even if you disagree with the poster’s estimate of the American Muslim population). Emphasis mine:

As an American Muslim, I appreciate what the President is getting at. But it is a bit of an exaggeration to say that the US could be considered one of the LARGEST Muslim countries in the world. There’s still only less than 10 million of us (typically anti-Muslim bigots tend to give the lowest, low-ball estimates, while identity politics playing leaders within Muslim communities favor higher end estimates). Besides, the US is SECULAR, democratic country, not one defined by ANY religion, “racial” or ethnic group. What he perhaps could have said is that the US is one of the freest and best countries in the world to be a practicing Muslim, or for that matter a member of any or no religion.
— Naj