When I first started becoming interested in comic fandom, I wrote an essay about the "stages" of fandom, and how a person becomes a comic fan in the first place and "evolves" from one stage to the next. It was never published (thankfully -- it comes across as more than a bit sophomoric in retrospect) but I still hold to some of the basic ideas I presented in it. The reason I bring it up here is that writing that piece forced me to examine my own history as a comic book fan, and reflect on my own evolving tastes.
The comics that really grabbed my attention as a kid were mostly now-classic Superman and Batman comics from the early 1970s. At the time I wasn't very discerning about whether I read them in Action Comics, Detective Comics, Justice League, World's Finest or whatever. (But to this day, I think Curt Swan is the only Superman artist worth seeking out.) Eventually that led to more "advanced" comics like Fantastic Four and Avengers. Jack Kirby's legal art-fight with Marvel was headlining comic news by then, and I started seeking out more information about the creators behind the comics and how they created the comics in the first place. Which eventually led me to Scott McCloud's Understanding Comics.

(That comic was one of five I made for that original essay. The odd panel structure was patterned after the lightning bolt on the chest of Captain Marvel, who I used as one of the narrative hooks of the essay.)
But what Understanding Comics has showed me -- a point which I didn't realize before -- was that I had been a fan of superheroes whose exploits were frequently delivered in comic book form, and not comics themselves. It was quite a revelation for me at the time (you might say it was like I was struck by a bolt of lightning) and it marked a very clear turn for me to actively seek out good comics not just good superhero stories presented within comics.
In my research at the time, I was discovering, too, that many fans experienced similar transitions. Not necessarily from reading McCloud, but from reading some comic that suddenly opened their eyes to the possibilities beyond what they had been reading. Not everyone experiences it, naturally, and those that don't are the ones who primarily read superhero books and don't care for "art comix".
And there's absolutely nothing wrong with that.
But that's why there's a divide between these two camps. One group of people are fans of the medium of sequential art, while another are fans of superheroes who happen to be frequently sold to them in comic form. And because they're primarily digested as comics, the reader assumes (as I once did) that s/he is a fan of comics. The primary vehicle for their enjoyment is being mistaken for the subject of their enjoyment. (And let me make myself perfectly clear that I'm not making any value judgments with that statement. It's an easy mistake to make, and one that I made for nearly 20 years.) I was talking just the other day about how the "comics" industry is largely a "superhero/fantasy" industry that happens to include some comics.
And that is where the conflicts stem from. While both groups are using the same terminology -- scripting, line weights, page layouts, etc. -- they're speaking different languages. One group is applying those terms to and discussing them in relation to a medium, while another is applying the terms and discussing them in relation to a genre. So when one side claims Maus as a great example of comics, the other is left confused because they're applying genre criteria to a work outside that genre. Conversely, a group lauding the workmanship in X-Men confuse the other side because they're applying the full range of considerations for the medium against a specific genre piece. Same words, different languages.
These misunderstandings can (understandably) lead to anger and resentment, and further divide the two groups. It becomes an us/not-us scenario and, coupled with some of that anger, gives rise to a "if you're not with us, then you're against us" mentality. And, naturally, if somebody is always against you, you're going to quickly take a defensive posture when dealing with them. It's almost instinctive. You ever read Lord of the Flies?
I'm over-emphasizing the schism (I hope) by referencing William Goulding's novel, but the basic premise remains. People dislike what they fear; they fear the unknown; and they associate the message with the messenger.
"I don't understand what you're saying. I don't know how to interpret your message. I don't like your message. I don't like you."
That's a bit overly simplistic, but I think that's what it amounts to.
Now me? I come from the superhero camp originally, so I understand that side of the discussion, and I don't harbor any misunderstandings about what that group is talking about. If/when I read something whose author clearly is writing to that mentality, I put my own, well-worn superhero cap on and read with that mindset. If/when I read something from somebody writing to the "art comix" crowd, I put on that hat and read accordingly. I expect most people who grew up on superhero comics, as I did, do the same thing.
But if you come to comics via, say, an art history background. Maybe via William Hogarth. Or through Egyptian hieroglyphics. You might not have any background/understanding of that superhero fan perspective, and respond to one of the "likes capes; hates art" folks with that same mix of confusion and anger.
"I don't understand what you're saying. I don't know how to interpret your message. I don't like your message. I don't like you."
Maybe I don't read superhero comics any more, but I have spent most of my life in fandom engrossed stories about people with fantastic powers wearing spandex. I still have fond memories of watching The Super Friends and The Batman/Tarzan Hour. Michael Keaton remains my favorite Batman. I still wear t-shirts sporting Fantastic Four artwork. 62% of my own comic book collection was published by Marvel. I own DVD collections of Wonder Woman and The Greatest American Hero. But I also enjoy the works of Joe Sacco, Jim Ottaviani, Spike, Windsor McCay, Bryan Talbot, Bill Watterson, George Herriman, Jane Irwin, and a host of other comic creators who rarely, if ever, made/make superhero comics. And I don't think there's anything wrong with that.