JIHAD IN THE KORAN
What about those who believe that all this god stuff is nonsense? They are not identified in the Koran, per se. This may be because in the Prophet’s time there was no such person. Everyone was assumed to believe in one or more gods or goddesses or some form of omnipotent being. Atheists, by definition do not believe that humanity has an all-powerful invisible creator friend running—and often ruining—lives, as God readily admits to doing on many occasions. However, if Allah had deigned to explicitly single them out as a group to warn future generations about denying His existence, they would certainly have been at the top of His Enemies List, and deservedly so. It is one thing for a god to refute the reality of other gods and goddesses; it is quite another for a wretched human being to repudiate any and all gods.
Allah, in His Koran, may not have explicitly singled out atheists, but Muhammad's son-in-law Ali certainly did; he burnt them, even if God’s Messenger disapproved of the method used, though not the killing.
Some Zanadiqa (atheists) were brought to Ali and he burnt them. The news of this event, reached Ibn 'Abbas who said, "If I had been in his place, I would not have burnt them, as Allah's Apostle forbade it, saying, 'Do not punish anybody with Allah's punishment (fire).' I would have killed them according to the statement of Allah's Apostle, 'Whoever changed his Islamic religion, then kill him.'"