Would the US allow a Muslim to fly Air Force one ?
How do you know one hasn't already? The answer to that, of course, is that you don't. Ridiculous question, really, as no religious or personal loyalty test can be applied to any such position. However, the Air Force's religious problems have generally been with fundamentalist Protestant proselytizers, so it is probably unlikely it's occurred.
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.