Muslims aren't out there differentiating themselves from the fundamentalists... they just aren't doing it. You could perhaps point to one or two that are speaking publicly about the matter - differentiating themselves, denouncing the attacks, and denouncing Muslim fundamentalism. But even those few who have spoken out are also saying that they "understand why we were attacked". What the hell is that?
Islam will continue to be blamed, rightly so or not, unless and until Islam differentiates itself from the "bad guys".
Why hasn't mainstream Islam stepped out and made any concrete remarks? Why is the Islamic world so wishy-washy on this? That's a real problem for non-Muslims. How the hell can mainstream Islam NOT step out against this?
And don't tell me they are - they aren't. Until such time as Muslims take some action, it is both rational and prudent to fear Muslims. There is nothing xenophobic about fearing those who have sworn to kill you... particularly if there is no denial of wanting to kill you!