I would agree that the use of nukes in WW2 was justified. The civilians living in Japan were knowingly under a state of war with the the Allies. While of course there were likely some dissenters, and some were probably at varying degrees produing towards Japan's war machine, the country was operating under a state of war. All the the citizens knew it.
Thus an attack on Japan, no matter how large was expected. Whether is was a few dropped bombs by the US or an outright in invasions, lives would have been lost.
The difference between this scenario and terrorists, is that it is no longer a question of state (with the exception of perhaps Iran and the previous government of Afghanistan which is another matter), nor is it a question of majority, nor is it a question of a declaration of war. You are now fighting individuals and I will indeed go back to suggesting one takes a look at my previous analogy about criminals in the United States.
The War on Terrorism is no war. It is no more war than the War on Drugs or the War on Poverty. These "wars" will have no declaration to mark the end and no surrender to mark the end. When you extend fighting terrorism to open and attacks on innocents Muslims or committ acts as suggested by Rep. Tom Tancredo, you are no longer protecting your country from terrorism, you will be inciting genocide.