In my opinion, chaplains exist to disciple and promote faith of some sort, usually in a deity.
Atheists, at least broadly, reject belief in deities to my understanding, although not belief itself. Atheism seems pretty broad from what I know and is not necessarily one set of beliefs. Therefore I don't think so. I believe they should provide counselors and support groups for anyone who needs them, but its not quite the same thing.

Elizabeth Backstrom majored in journalism at Western Washington University and currently works as remotely as a grant writer. Her background is in news writing and features, but if an overabundance of caffeine is consumed, she has been known to write a humor piece or two. Backstrom attended various Christian churches growing up in Washington State and in her free time enjoys reading about history, religion and politics.