I have refused to remove my shoes when I know there is no metal in them and when it is obvious that the floor is dirty (and I am barefoot within my shoes). I see no reason why I should dirty my feet and expose them to various fungi. Generally, I receive no secondary inspection; once I did. So be it; it is better than filthy feet. In Japan (or was it Korea?), when you are asked to go thru a security checkpoint barefoot, paper is down on the carpet and you are given plastic shower slippers for the walk thru the x-ray.