Moslem-Americans are pretty loyal as a group, and their integration is all the more remarkable when you consider the views of Moslems in Europe and the record of ethnic minorities in America in past conflicts. And the length of time we have been at war with jihadis adds to this good record. It helps that there essentially has been no backlash against Moslems here, despite CAIR's blithering idiocy on the matter and our coastal liberal elites' constant worrying about "clingers" (guns and God) in fly-over country.
So when we look for jihadis in our midst, it isn't a sign of the coming repression of Moslems. And when we find someone who has betrayed us to support jihad, it doesn't erase the general truism that as a whole American Moslems want nothing to do with terrorism.
And never forget that having loyal Moslem Americans is an asset when fighting jihadis, just as having any loyal immigrants from a country we have been at war with has been.
Strategypage has an excellent post with an overview on this subject, with a good summary of the World War II ethnic Japanese issue. Yes, there was a reason for what we did, even if FDR over-reacted.