Read Jeff Sparrow's the global war on witches, a convincing comparative study of the early modern European witch craze and the current 'war on terror'.

The WOT is of course a persecution of Muslims. This seems to make it different from the witch trials. Of course, witch trials were partly about cultural and religious non-conformity. One could indeed argue that they were in reaction precisely to the Muslim threat at that time – gates of Vienna and all that.