There is a difference between religion and Witchcraft.
Witchcraft is a spiritual practice, religion/paganism (both of which are technically the same) is a belief in some sort of divine, spiritual presence.
Some religions call for such things that involve, what many would consider, witchcraft. Christianity, Wicca, and so forth does call on this. However, the execution of, should I say, spells, are different from one to another.
That being said, witchcraft being a practice, you can practice it and be atheist. Of course, you have to believe your doing something, whether some form of placebo or the power you have over the universe. It is a common misconception to believe that in order to practice witchcraft, you have to believe in some form of spiritual being. And being a witch does not mean you worship the Christian Devil.