Answer:
No. The War on Terror has many complexities to it, so being against it is not in direct correlation to being unpatriotic. Especially if the reasoning is being a pacifist, a right guaranteed to anyone by the U.S. government. It is, however, unpatriotic to not criticize a country doing morally questionable things, as is told for the people of the U.S. to do if it has become corrupted.