Dave, I will see if I can out of context summarize the conversation so that The Best Show reference makes sense.
Of course it Mort Marons so their is the ever-present "this always has to circle back to me" current running through his conversations. Jesse Thorn and Maron were discussing the proliferation yet de-centralization of geek culture, and how neither of them feel at home with or self-identify as geeks, though they would classify themselves more closely with geeks than jocks. At 47 you would think you would have made peace with your station socially, but that is neither here nor there.
Maron says that he feels more pressure and judgement these days from the geek culture camps that have formed because of the internet, and to be specific he called out (not by proper name) FOT's as the camp that have given him "the most shit". It seemed almost as if he had been reading the forum posts about him, and that was the criticism he was referring to. He actually said that it kind of hurt his feelings, and that he would like to have overlap with Tom's audience, but he felt that some of Scharpling fans were part of some super geek, pseudo-intelligentsia. Thorn then postulated that the deep commitment that fans of The Best Show have in the program can create a blind spot in some fan's eyes, and the dick's that are Best Show fans are quick to "give shit" for no reason. Both mentioned that they are realy Tom's friends and think it is silly that they would catch guff from the Best Show crowd, as they both like the show. Maron made it clear that he was kind of jealous of the FOT fervor.
Honestly, they were both being complimentary to both Tom and the Show. Marc wasn't being confrontational or condescending. I think he was just asking why he would be catching shit, from what perceived to be somehow an organized effort by fans of something that he himself likes.