Right, religious beliefs are far more complicated than atheism. This is because atheism is merely a lack of belief in a deity, while religious beliefs usually include far more than just believing that a certain God exists. And, if you put up a story saying that an atheist man raped his daughter and blamed his lack of belief in a deity on this behavior, it would be ludicrous. That is, unless you could provide some objective evidence as to why you feel there might be a correlation. I think that would be an impossibility, but I would definitely be open to discussing it.
As for this incident, whether you like it or not, this woman was killed because the crowd thought that she burned the Quran, which seems not to be the case at this point. This is certainly related to Islam because the Quran is not held as "sacred" to any other religion than Islam. Also, the men committed this crime because they felt that Islam was insulted figuratively. While I agree that these men were following rules that don't seem to be an accurate interpretation of Islam, it cannot be said that they did not have the teachings of Islam in mind (at least their own interpretations). On the contrary, you might be able to create a line of reasoning that leads you to believe that an atheist's actions were caused by their lack of belief, it would not be direct, because the atheist would, most likely, not use his atheism as an excuse. This is what we have a major problem with in this thread. Islam is used as an excuse or reason for violence by the criminals themselves, which is unacceptable in many ways.