japan is a country. the difference is that islam is a set of political, religious, and cultural beliefs, but it is not a country. in fact, islam spans international borders, and is considered paramount to mere nationalism.
so, the FDR/WWII analogy loses application almost immediately.
Simply stated, Bush was what I consider a traitor to the USA, putting his bin Laden friends before America. What reinforces this is the Bush speech two weeks following 9/11 where he went before the nation and spoke about the Islamic people, the good Islamic people.
Can you imagine FDR addressing the nation via radio, and saying, look America, the majority of Japanese people are are good people. How long do you think he would last before he was strung up to the nearest tree? I doubt a single day!