Atheism vs. rationality
Although they are commonly seen as going hand-in-hand, atheism and rationality are two different things.
Connections between atheism and rationality
Certainly, there is a perception that atheists stand for rational thought, belief based on evidence, and healthy skepticism. This view is helped by the fact that many of the more vocal proponents of atheism, such as James Randi and Richard Dawkins, are also proponents of skepticism and rationality, and by the fact that there does seem to be significant overlap between the two.
The path from rationality to atheism is a simple progression: one may start by questioning the existence of Santa Claus, fairies, telepathy, etc., and rejecting those beliefs based on the absence of empirical evidence for them. It is logical, then, to take the statement "there is a god", subject it to the same scrutiny, and arrive at the conclusion that there is no good empirical evidence for any gods, and discard belief in gods along with fairies and other supernatural ideas.
Differences between atheism and rationality
On the other hand, humans are good at compartmentalizing their beliefs. A person may rationally conclude that fairies do not exist, based on lack of evidence, yet fail to apply the same reasoning to other cherished beliefs, such as telepathy or God. Many scientists who are also theists fall into this category.
Conversely, one may rationally conclude that no gods exist, based on the lack of any evidence for them, yet fail to apply this reasoning to other beliefs, such as the healing power of crystals or reincarnation.
Taoism and Buddhism are examples of atheistic religions: their adherents may believe in any number of things that are not supported by empirical evidence, such as souls and reincarnation, but not in any gods.
Application to arguments
One common argument against atheism is that some of the worst atrocities of the 20th century were committed by atheists such as Stalin and Pol Pot. While it is true that these people were atheists, it is difficult to find a causal link between their atheism and their genocidal actions; it is much easier to find a cause rooted in some other, irrational belief, such as the inherent superiority of communism, paranoia, or cult of personality. In fact, it is much easier to argue that the worst atrocities of the 20th century were committed by people who held irrational beliefs. This is one case in which it is important to distinguish atheism from rationality.