The problem? Well, while it sucks that the hardcover collection wasn't allowed onto the list, I understand why. Graphic novels are not the same as traditional novels. They're visual and while there tend to be very in-depth and fascinating stories behind those visuals, they simply are not the same as traditional novels precisely because they do not rely entirely upon the writer's words in order to succeed in forming an image in the reader's mind. Traditional novels only have words to work with. To try to compare a graphic novel to a traditional novel would be like trying to compare flying in an airplane to riding on a bus. As such, you can't really put the two on the same list. It wouldn't be an adequate assessment of the material.
That being said, it's entirely reasonable to desire a graphic novel/comic category for the bestseller list. This might take time, but I would think that such a category would be a good thing. I happen to like graphic novels (and comics, although I'm more favorable towards the former), but I do understand the reason why they don't end up on the New York Times Bestseller List along with traditional novels. It's sort of common sense, you know?