As Maddow pointed out last night, many of those protesting believe that the lack of censorship of the anti-Islam movie on our government's end equates to our (U.S.') support of its message. The majority of Americans couldn't care less, let alone understand what's going on, but that's not easy to explain to someone whose idea of Americans' views may be shaped by something other than accurate reporting. In addition (and I don't speak from any personal or related experience), I think the concept of free speech and it's occasional side-effects may be completely foreign to someone raised in a Muslim nation, taught to respect Muhammad/Allah above all else, with zero tolerance for their criticism.
I think we face a potentially big problem for our future, seeing as this may not be the last time something like this comes up. A quarter of the world's people are Muslim and many Muslim nations pose a challenge (or opportunity, in cooperation) resource/military-wise, and I believe it's critical that we find some way to not appear disrespectful. I believe it's the government's role to act accordingly and consistently.
Christian ignorance doesn't help either. 9/11 was viewed as an act of extremism, but an attack during sustained anti-US protests could have much broader effects, primarily in shaping the reaction of a large portion of Americans.
As an aside, Bachmann/McCain's comments about Muslims and Muslim-nations (or what the media makes them out to be) are working completely against what I believe should be our goal. I see absolutely no support in mending this issue from the GOP, only ignorant comments and threats to the nations in question.
Thoughts? Would really like to hear some muslims pitch in, I know we have a few on the boards...