I've always liked this particular meme. It manages to be silly while simultaneously poking fun at Christians for some of the absurd things they believe about atheists. And yes, that is my take on the primary meaning of this meme: it serves to highlight the absurd lengths to which some Christians will go to demonize atheists.
"But do any Christians really believe that atheists eat babies?" Although this isn't the point of the meme, I suppose it is a fair question. I suspect that if you take a moment to consider some of the things many Christians at least claim to believe, this one will strike you as at least somewhat plausible. If not believing in their preferred god(s) makes us immoral, evil, and almost certainly Satan worshipers, is it really that much of a stretch to assume that we probably eat babies too?
Remember, these are the people who brought us the moral panic over Satanic ritual abuse. They convinced themselves that Satanic cults were operating in almost every town in the U.S., abducting, sexually molesting, and ritualistically sacrificing children. The lack of evidence certainly didn't stop them from ruining some lives along the way. And remember, many of these same people are quick to tell you that they would run wild in the streets, raping and murdering whoever they encountered, if they found out that their god did not exist! So yes, they seem to believe plenty of strange things.
Of course, no mention of baby eating should omit the fact that there are several references to the delightful practice in the book which some Christians still claim to be "holy." In fact, the Judeo-Christian god appears to be incredibly fond of punishing people by making them eat their children. I suppose this should not surprise anyone who has read this particular book. It is filled with examples of this "loving" god commanding murder and genocide. Children are rarely spared, and parents are often instructed to kill them.
From what little I still recall from one of the religion courses I had to take in college, early Christians regularly accused Jews and Muslims of eating babies and demonized both groups with such accusations. With the many biblical references to the eating of children and some early fears about non-Christians engaging in the practice, there seems to be sufficient basis for bringing it up as a point of mockery directed at Christians who insist that our atheism makes us evil.
It does not matter all that much whether modern Christians believe that we eat babies; plenty seem to believe that we are morally inferior and should be treated as such. And as long as that remains the case, calling attention to it through humor seems appropriate.