You are addressing different questions here, one of them is the Theodizee problem: How can terrible events and suffering be explained if God was almighty. There is no simple answer, this is why I think most members of my church at least are in a certain doubt whether God exists but still try to hold on to their faith and at least listen to the message of the New Testament. So in fact, there is no black and white in terms of naive believers versus atheists, but many people use their brain and still want to be reminded of the values conveyed by the New Testament.
About killings, of course I'm not responsible for any crime of an extremist just because he/she claims to commit it based on a certain interpretation of a religion. No peaceful muslim is responsible for crimes of extremists, and he/she should of course NOT feel ashamed just because the terrorists claim to refer to the Koran. I think this is so self-evident it is not even worth mentioning.