Don't get me wrong - I think we should have the freedom to draw whatever the hell we want and be free from threats of deadly force. I think all the people who threatened physical harm to the original cartoonist are despicable, but this way of going about it is frankly extremely damaging.
Note: I am not Muslim, I am an atheist, and I want to apologize on behalf of atheists who have unfortunately chosen to participant in this disgusting farce. They do not speak for all of us. But, moving along...
Most Muslims are against violent reprisal. Are they offended? Yes, but like every other controversial issue in the world, only the extremists would go to the end of harming someone. The internet community that has fueled the popularity of EDMD is ignorant of this, and their numbers are muddied by the many racists and bigots also in participation for the wrong reasons. It's like if the KKK showed up at your political protest - there goes your credibility. As organizers of a principled stand for your rights, you need to make sure that your group cannot be conflated with racists, bigots, and other nasty people. The community around EDMD has done an extremely poor job at it (IMHO mostly because a lot of the core people spreading this around are themselves racist).
It is, frankly, juvenile, especially once you read some of the discussion by people who actually are participating in this.
Imagine if a group of atheists firebombed a church for making fun of atheism, and the Christians' response is instituting a "mock atheism day". Does this solve any problems? Does it create more understanding? Does this help improve the view, from either side, that most people are actually reasonable, sane people?
No, it simply promotes more polarizing viewpoints, more extremism, and eventually more violence from both sides. It is counterproductive and I'm embarrassed that so many atheists, who like to proclaim themselves freethinkers, have gotten on this bandwagon.
This isn't a principled stand in response to extremist action - this is an indiscriminate melee of offensive content that is not targeted at the groups and people actually responsible for making threats against people's lives for their expression. Speaking to my Muslim friends, they are as appalled by the violence of extremists as we are - the correct course of action is to work with moderate and liberal Muslims to combat the actions of extremists, not to alienate and offend the allies we need most.