because the vast majority of people are intelligent enough to not get upset about cartoons alone.
I imagine the thugs who shot up the office were very very upset about the cartoons because empty people end up filling their lives with platitude based ideologies.They don't have a particular "understanding" of the religion they use, any more than the anarchist who shot President McKinley had a deep understanding of anarchist literature or that Gavrilo Princip was an intellectual icon of Slav nationalism. They saw a way to enter the history books (and have their 72 virgins) and took it; because have a deep-rooted lack of purpose that is easily fulfilled by the "charm" of chaos.
Blaming things on religion is a silly response. Sure - the prospect of martyrdom is unique to religion, I'll give you that. But terrible people will continue to be terrible regardless of the religion they attribute their actions too; and vice versa.
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And of course I ignore the other players: the faceless men who fund these idiots and spread violent ideologies across the globe. Of course, that can be blamed on religion; but a faith that predates Islam : the worship of Mammon.
Thousands, probably millions of people called for the Muhammad cartoons to be censored. Millions of people, majorities of entire countries, support executing apostates and all that other horrible stuff. Do you honestly think all of them are terrible people (or at the very least unintelligent)? That just seems like an extreme, black-and-white view of the world. Not everyone who does terrible things is a psychopath or just a "terrible person." We all have the capacity to do or support terrible things. The idea that belief systems which claim to define morality and are taught to people as truth from birth can't significantly encourage/promote that capacity, because people who do bad things are really just inherently bad people, is ridiculous and Manichean.