Why would they be exempt when the goal is to convert everyone in the entire world? Not believing in any god whatsoever doesn't remove you from the radar completely. They might even find them to be far worse than people who actually believe there is a deity at all.
But this is all speculation really. I wasn't there, and I'm never going to follow "Allah".
Actually no, there is not that much of killing and violent verses in the New testament, Jesus if he ever existed was more like a hippie in comparison to muhammad who was a bloodthirsty invader and pedophile.
This equality that all religions (not in the sense of historical part) share same level of violence in their teachings isn't true, some religions can be very pacifist comparing to others.
Oh atheists are even worse off than the Christians in Muslim countries. Muhammad said that Muslims should not kill ''People of the Book'' (Christians, Jews...) who submit themselves to Islamic rule and law. He did not say the same thing about atheists.
During the Soviet-Afghan War, the mujahideen summarily executed nearly all atheist Afghans, for the believed that the atheists would be allied with the Afghan Communist Party and the USSR. This hate towards atheism is still rife in the Muslim world.