Humor, for what it is worth, is almost impossible to fully explain (though the confusion of expectation seems a regular part of the humor - cognitive dissonance, in other words.) And so often it manages to strike a nerve. If the joke "works," it strikes the nerve and calls the object to mind without causing true offense, we may act offended for the sake of social pretense, but we aren't actually hurt.
But equally possible, it could hurt. It could bring to mind something, possibly something it didn't even aim at, and cause little more than trauma. The fact is, we don't fully know the contents, or more to the point, the history of most other people's minds, and it is almost inevitable that any joke that hits close to home will in fact not so much hit too close to home, as hit a bunker somewhere in the back, full of munitions.
There's nothing to be done, really, in such cases but state ones actual intent, and for the person to realize that you may have still paid an unintentional favor: pain, when it serves its evolutionary purpose, is there to alert us to a problem. It can say, "hey! Look, something else for you to work with your damn analyist on!"
But seriously folks, the point ultimately is not that we should stop joking. It is that we should have compassion for one another at the same time. When joking makes us lose our compassion, when it becomes a front for coldness and allows us to distance from others, then it really is just a prelude for rape, even if it is just rape of an emotional kind.
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