My guess is the reality is that profilingof Muslims is inevitable, and goes on even if not acknowledged.
In fact it may be rational to an extent, and even draws support form odd places, for example today with respect to Islamic terror and how to deal with it.
Nonetheless if we go this explicitly way it should be very carefully. Muslims have helped us to capture many Muslim terrorist and it is crucial to not alienate all Muslims by treating them as terrorists. While I think President Bush made many mistakes in the War on Terror, he did understand that not all Muslims are terrorists or sympathize with terrorists. Let’s continue to apply his wisdom on that.