My background: I've been reading Penny Arcade since 1999, I've been reading feminist blogs since the invention of blogs, I am intimately familiar with the way internet arguments escalate, and I have a sense of humor. My take, which you should understand is the correct take from what a fucking expert I am on all these topics, is that PA made a perfectly appropriate rape joke which no one ought to have objected to, and then a funny comic mocking the concept of rape culture, and then a series of increasingly swinish moves, followed by an absolutely stellar apology. Pretty much everyone else has behaved execrably.
Out-of-context criticism is absolutely endemic to feminist blogging, and I think it's because expressing solidarity for rape victims outweighs pretty much any other concern including accuracy and fairness. This is a value feminists have: if you asked most feminist bloggers what motivates them to blog, "because somewhere, a woman is being forced to have sex against her will" is going to be high on the list.
But qualities of the crime of rape are variable and resist conforming into an overarching social narrative of cause and effect, whether this narrative is "rape culture causes rape" or "women's rape claims are strategically-motivated". Proponents of each narrative have their own shibboleths and very little patience for views or data that fit their narratives badly. And why would they display patience? Either there's a world of women whose lives have been destroyed by rape, or a world of men whose lives have been destroyed by false accusation--in either case, the appropriate response to this terrifying world of arbitrary injustice is outrage and activism.
My personal, meaningless opinion is that there are probably numerically more rape victims than falsely-accused rapists in the Western world, but it would certainly be easy to receive the opposite impression. False rape accusations have inherently longer news cycles, for example, and tend to leave believe-the-victim feminists looking credulous. Also, my high-school sex-ed teacher has by now taught generations of young men that a woman whose lips have touched even a single drop of liquor will be fully supported by society and the legal establishment in railroading any young men who foolishly have sex with her to federal pound-me-in-the-ass prison.
I suppose reviewing rape conviction rates from reality would have conveyed the impression that you could do quite a lot of rapes without fear of prosecution, and so I see why she presented this nugget of men's mythology instead--still, it joins the pinpricked-condom and half in undergirding a worldview where relationships with women are a threat. And the complementary worldview in which men are a kind of deadly animal who mainly abuse, rape, stalk, and discriminate against women is, of course, prevalent in its own circles.
Now, on the internet, these ideologies are taken up by people whose knowledge of the nuances of their apologia vastly outweigh their experience with, e.g. the mechanics of sex, and so everything is really angry and stupid and broad. In the case of feminist blogging, I've seen this translate into a practice of defending the notional traumatized rape victim at all costs (for example by tagging up every fucking post with "trigger warning"), even against actual rape survivors who, after all, are women who continue to live and crack wise and have idiosyncratic opinions even if the rhetoric we use tends to present them as broken or no longer fully human ("lives destroyed" earlier in this post, for instance). For the video gamer, it is probably fairly difficult to transition suddenly to the feminist version of a term ("nonconsensual sex") which is in ubiquitous use in his subculture as a synonym for "defeat soundly", and in general use as something more like "sex obtained at knife-point, by a psychotic stranger, from a jogger". The gulf between definitions, not to mention the existence of complete assholes on various sides, makes some kind of conciliation between ideologies a seeming impossibility.
I'm not sure that I can bring all this together to some kind of conclusion. I'm not sure anyone can. I'd like to see everyone treating the person glimpsed through the screen like they were sitting beside them, but I don't exactly follow this precept in my own online conversation, and I am a bit of a dick IRL besides. And I'd like to see fewer rapes and, I guess, fewer false accusations of rape. I suppose I can do worse than conclude by quoting Tycho: "Go, and rape no more."