Look, Penny Arcade has a problem. On the one hand, they want the freedom to write absolutely anything they want in their comics without being criticized for it and anyone who doesn't like the comic can fuck right off. On the other, they want PAX to be a welcoming and inclusive place especially for sub-groups that have previously not been well-represented in the gaming community such as women, hence the banning of booth babes, and they don't want anyone to feel threatened there or made to feel uncomfortable.
There isn't inherently wrong with either of these goals. On a general level, I think most people would support both. And if they were capable of separating PA the comic from PAX the convention entirely, this probably wouldn't have been as big a deal. But unfortunately, there is overlap between them, and Mike chose to respond to a controversy in one of them with his mindset from the other (probably because he doesn't really have any other way of thinking). The comic received criticism on a handful of feminist blogs but no more. That was it. But rather than attempt to engage them honestly or even just ignore them (everyone saying feminists should simply not read Penny Arcade if they're offended by it is displaying a staggering lack of self-awareness), he chose to antagonize and mock them and his fanbase took up the cause. If you're going to respond the way Mike did to some bloggers criticizing your work, you don't get to tell anyone else to grow a thicker skin.
But even that wasn't enough, he had to make the shirt and then sell it, and then encourage people to wear it to PAX and brag about him wearing his own. Let's be clear about what this signified: It was a blatant "fuck you" to all of the women and actual sexual assault victims who had expressed feelings of discomfort about rape-related humor. No, it was not a banner of free speech or brave and noble weapon to wield against the scourge of censorship; if you have been told explicitly and in no uncertain terms by a group of people that "This joke makes me uncomfortable and here is why" and you proceed to make a shirt embodying exactly that joke then there are only two possible conclusions: 1) You have the short-term memory of a goldfish, or 2) You are deliberately intending to make those people uncomfortable. You have found their weak point and you intend to exploit it. You cannot claim ignorance or naivete as an excuse; you have been informed of how these people feel and you are using that knowledge to your advantage.
And hey, PAX is their convention. They have the right to do that. They have the right to flagrantly disregard the comments of actual women who expressed concern about how it would make them feel to go to the convention surrounded by people literally wearing rape joke T-shirts. They have the right to say that the convention will be just like the comic, a free-for-all for rape-related humor and anyone who doesn't like it can fuck right off, just like they should with the comic. They absolutely have every right to run PAX with the same mindset that they write their comic.
But then they don't get to claim that PAX is inclusive and everyone is welcome. They don't get to say that they want to make sure women are not made to feel uncomfortable the same way they often are at other conventions. They don't get to say that they care about PAX being better than other conventions about this. The dirty little secret that they never realized is that free speech and making people feel welcome are both perfectly noble ideals that are in conflict with one another and if you choose to side with the former in every possible circumstance, even if it means antagonizing rape victims, even if it means alienating women, even if it means going against your own stated goals, then you're not a martyr for free speech. You're just an asshole.