Frankly, if you have to ask why should people get so up in arms over rape games when there's so much killing in others, you're either fanatically devoted to that asinine philosophy that everything's a matter of opinion or you're suffering from a brain tumor.
As the above article stated (though I think its tone was slightly cynical), comparing rape to killing isn't really the same because the actions aren't equivalent to each other. Killing is sometimes an unfortunate necessity, while there's never a legitimate reason to violate someone sexually. Perhaps rape can be included in a game as part of the storyline, i.e. a you play a cop trying to catch a rapist or the hero is hunting the antagonist because he raped his girlfriend/wife/loved one, but never as an activity you engage in.
I believe in the freedom of speech and that people should be allowed to say what they wish. But never forget the door swings both ways. The way I see it, everybody has the right to say what they wish, no matter how offensive, just as those they offend have the right to verbally tear them a new one.