Don't misunderstand, Atheists spread this joke around, too. And I'm willing to bet that some people believe that we do indeed eat babies...They are particularly good with barbeque sauce. emotion_dowant
Atheists are thought of as heathenistic, heretical, immoral people (some even go so far as to say we aren't even human). It most likely comes from the so-called "pro-life" side joking (or rather..not-so-joking) about our "baby-killing" ways.
It seems to be more of a joke when Atheists are talking about eating babies rather than theists, though.