But the label that religion makes people do bad things is as ridiculous as video games makes people do bad things.
People do bad things to do bad things, they just find whatever is convenient to justify or blame it on.
I agree with that to some extent. Religion and nationalism are very similar, in that they are typically based on developing strong self-identities that exist in relation to some clearly defined "other." But from this, it is not difficult to begin viewing the "other" not only as something less "good" than the self, but as less than a person. This is what soldiers are explicitly taught to do with regard to their enemies.
Religion can do the same thing. Now, would Islamic extremists behave the same way that they do without religion? Perhaps, but the alternative would require strong local identities of some kind (since these individuals don't have state identities to speak of), or strong adherence to some ideology (like Communism, though this only works in certain cultures with specific histories re: class conflict; or fascism, though this is often built upon an existing "state" identity) and it is much easier for warlords and politicians to exploit religious ideas and fears in order to rally support over that of some more abstract "communal identity". The idea of religion is easy to understand, helps us to alleviate many of our conscious and unconscious fears about reality, gives us clear purpose, and as such, really helps to overcome issues such as organization and the "collective action problem." So, it can be used to make bad things happen more frequently, and more efficiently, than they otherwise would.
Would people do bad things without religion? Undoubtedly. But organized violence would be less frequent, particularly at the sub-state level, where those who want to control don't have the resources to use fear and intimidation as a means to persuade. Of course, religious zealots could then be used to create fear in the populace, which then makes the religion idea less important than it initially was as this becomes a self-perpetuating process, and you have stuff like you see in Africa.