Personally I have no qualms with Penny Arcade. I get that their (and when I refer to "they" I mostly Gabe and Tycho) sense of humor may not appeal to everyone and I get that they sometimes say things which seem or are inappropriate and offensive but I think that collectively we get hung up too much on some of their worst moments and we're too quick on pulling the "you're dead to me" trigger.
I don't get this preconceived notion that a lot of people seem to have that just because someone is successful or famous in their line of work it means that they should act a certain way or show an increased level of maturity and respond in a stone-cold manner.
Whereas with some celebrities we'll treasure and celebrate their honesty and down-to-earthness, like Jennifer Lawrence's, in some other situations like Penny-Arcade's we'll almost outright demonise them for isolated moments of unadulterated honesty.
I don't think that anyone is perfect: not Tycho, not Gabe, certainly not me and I reckon certainly none of us are, the only difference between the arguments you might have with a random person on the internet and them is that they are giving their public face away and they are mostly honest about it. Warts and all, it's who they are. Whereas that random person you disagree with on some form can ignore you completely and move on, every word they say falls under public scrutiny. Modern social websites are tools that can help bring a lot of good, but are ultimately used many times as places to hold public lynchings against individuals or companies.
Ultimately I think that Penny Arcade has been very good for games and gamers over the years. When interest in consumer-based gaming expos was withering, they helped revive it with PAX, when gaming journalism was under a lot of scrutiny and criticism they tried to make a new game site with more proper reporting. They also founded Child's Play and have helped various artists over the years. I don't think if they were as bad as some people imply they are, as a whole, they'd dedicate themselves so hard to gaming.
I don't think that their good deeds excuse their worst actions, but they're just people like you and I. The only difference, to me, is the magnifying glass over their heads.