Genre fiction doesn’t get an undeserved bad rap because genre fiction is itself is bad; rather, genre fiction has gotten an undeserved bad rap because genre fiction fans are so often undiscerning readers.
I think there's a lot of truth to this, for the same reason that any pop-culture phenomenon gets a bad rap: the audience.
I'm not just talking about people who throw cold-eyed sidelong glances at the kids in costumes queuing up in front of the convention center on the other side of the street. I'm talking about when fans are reaching for their smelling salts over ... other fans.
I had my most recent exposure to this after I finished watching and reviewing Fullmetal Alchemist: Brotherhood for About.com. I loved the series, but two of my close friends (who are both anime fans) could not touch it. Why? The fans for the show had made it impossible for them to do so. They couldn't set aside the rabid behavior of the fans long enough to enjoy the show just for what it was. I had my own bad experiences with Firefly and Serenity in the same vein: the fans of it within my reach refused to stop trying to sell me on the merits of the show, and by the time I got caught up with it I didn't see one-tenth of what they were gushing about.
That's my example. I imagine you have any number of your own to fill in: Hetalia, Harry Potter, My Little Pony, the list goes on. I'm not implying that I find the fandoms for any of these to be insufferable, only that I've heard the same from others, whether justified or not.
By and large, many of these shows and books are not bad. Some of them are quite good, and merit the time involved to investigate them — if you are inclined to do so in the first place. I find more and more often the "if" revolves not around the work itself but around the audience for the work, and that the assumptions about same by outsiders go unquestioned.
Some of this is the I Wouldn't Be Caught Dead With That phenomenon, where people shy away from something simply because of the possible social consequences of owning up to having been exposed to it. They loathe the idea of having to defend not even just liking it, but merely saying they read/watched it. In short, it's the intra-fandom peer pressure that makes enjoying such things on their own terms difficult.
There's a complicated problem here. So much of what goes on in fandom is fun because of the sharing that goes on with other fans. But if you find yourself at odds with the fandom for a given thing, sharing becomes exponentially harder because you don't want to associate with Those People — which means, you guessed it, you have one less reason for ever bothering with it in the first place. It's only fun up to a point to savor something all by yourself. Which would you rather do: see The Avengers in a theater surrounded by fellow fans, or see it all on your lonesome on your laptop with your headphones on? (Assume for the sake of argument the theater experience does not include someone kicking the back of your seat or throwing up into your hair.)
There are some things I'm a fan of that I feel more than a little self-conscious about trying to connect to other people through. My appreciation for someone like Yasushi Inoue is tough to communicate to people who haven't actually read his work — and the few that have mostly seem to be doing so in a wholly academic context, which is a damn shame. Nothing against people in academia, mind you — I just always feel like such a weirdo babbling about someone that esoteric, trying to explain what it is about his work that electrified me so much. So I confine most such blabber to this blog and leave it at that, instead of accosting people at random in Asian Studies departments. That's not so much a solution as a stopgap measure, though.