Judging from the article, Werwolf doesn't seem to have aroused any enthusiasm among the general population or to have drawn foreign volunteers into the battle. They seem to have been hardcore adherents of the old regime with little broad or deep appeal to most Germans who kept their heads down and got on with the rebuilding. Average Germans might have been less likely to work with the occupying powers, but that's about it. I don't know just exactly who is fighting against us in Iraq, but the potential is for a far worse situation than in Germany when one adds religious fanatics, foreign volunteers, and nationalist fervor to hard-core Saddamists.
At the same time, from 1945 to about 1949, there was also guerrilla fighting going on in Ukraine, Lithuania, Poland and elsewhere that was bloodier and more disruptive than what was going on in Germany. The Greek Civil War was even worse. It's too early to say about Iraq, but in the context of the times and in retrospect, postwar German resistance doesn't look like much.
there is very little to compare between post-war Germany and postwar Iraq. People don't seem to understand that we're making history not reenacting it.