The publication of fan fiction in fantasy and SF is nothing new. There are zillions of Star Trek books and short story collections, for example. Such fanfic stories are published with permission of the copyright owners.
But what about underground fanfic? A striking example would be "slash" fiction. Spock and Kirk become lovers. Seven of Nine hooks up with Captain Janeway. These stories are obviously not part of the Star Trek canon. But the Trek copyright holders will put up with slash fiction because the tales are intended for private, non-commercial purposes.
Fifty Shades of Grey by EL James is an interesting example of non-canonical fanfic being published for profit. This story has its origins in Twilight fanfic. The serial novel was then Master of the Universe, and the characters were named Edward and Bella. The chapters have since been collated and edited, and the names changed. Although the Kindle version is a whopping 9.95, it's selling very well.
I haven't read the Twilight books, nor have I read Fifty Shades, so I can't comment on the originality of the characters or plot. Clearly, fanfic can be so completely removed from the original characters and universe that the base story is merely a jumping off point. It goes without saying that Stephenie Meyer hasn't given permission for EL James to play in her universe. Stephenie never will. Because Fifty Shades is BDSM erotica.
Edward, now called Christian, is not a vampire. He's not a high school kid either, but a powerful business mogul. He's also a Dominant looking for a submissive. The vampire has been supplanted by the sadist. This is a valid replacement. Blood sucking in fiction has a lot in common with BDSM: pain and pleasure are combined, and offering blood can be considered the ultimate service.
Fifty Shades, irrespective of its origins, could well introduce a whole new set of readers to BDSM fiction. One reviewer says it's "an educational introduction to BDSM literature." I hope this book does kink justice.