Maybe the theist is simply insulting the atheist? Doesn't mean HE would rape anyone but he thinks you would.

But really you're just experiencing the Cut Flowers phenomenon of social decay. The link to our moral foundation (religion) has been cut, but there's still water in the plant. Over time this will decay and the plant will dry up, as each successive generation loses the moral basis for the rules they teach to their children and people become more decadent. That's not to say rape will become commonplace in high-functioning societies - but the legal system and risk of punishment or social stigma will become the driving motivation for not raping - so it will be more likely to happen in certain contexts where people can get away with it, or where they think others will look the other way. (famous or powerful people) This is all true now, but fear of God is one more check on bad behavior. It also requires more power in the hands of the state, whereas a moral people are able to live under greater liberty.

Empathy - besides being a genetically inherited trait as someone else brought up - is a contextual emotion that can be modulated by social rules. Plenty of rapists will convince themselves that the other person enjoyed it. As communication has shrunk the world, it's said that our "circle of empathy" has grown to encompass all humanity and basic respect for all mankind, but I argue that that's performative. We generally only have real empathy for our tribe or family. Protecting "our own kind" is the purpose of the emotion. If the social pressure forcing us to feign empathy for strangers ever goes away, it might end up that people see nothing wrong with using rape as a punishment against other nations, criminals, or whores. That has been a thing in some cultures. (then there's the retarded abbos that rape their own siblings...)

Since we're talking about a societal issue, there's no point in Othering the savages and saying YOU wouldn't rape anyone. That's great but you can't claim that for all of your tribe, for all time. It's only by the grace of God or dumb luck that we don't live in those times yet.