Pagans, to put rather bluntly, are theists of a different kind. Some pagans find/believe in the presence of god in the Universe, some in living beings, nature and acts of nature. It constitutes a lot of such beliefs. Atheists on the other hand, reject all conjecture that points to the existence of a God.
Pagans are mainly polytheistic or pantheistic. They are as much irrational as the other prominent religions in the world. The only difference is that they are not a significant organised religious force or establishment that has the potential to affect world matters. An atheist on the other hand does not believe in such irrational philosophies and myths. Actually the only similarity between atheism and paganism is that both of them do not have an organised form throughout the world.