When publishers buy fanfiction and repackage it for the mainstream market, they're making two big assumptions:
1. This book has an appeal beyond its initial fanbase.
2. This book's popularity in fandom says something about its potential popularity on the mainstream market.
And I’m not entirely sure those are good assumptions to make.
There is a very definite possibility that E.L. James was another Octomom; that she got big on notoriety rather than any real interest in her content. She wrote a story about something relatively taboo, and the way in which it was published was also (or at least it used to be) taboo. BDSM and intellectual property theft - turns out that the two of those things churn up enough interest to make you a bestseller.
This was the first time something this raunchy went mainstream. It got a lot of attention and started a movement. There's no doubt that E.L. kicked erotica into high gear and that a lot of other people have been successful in that field since. But I notice that all of the breakout successes since have been original fiction.
I think the forbidden unknown was the draw of E.L.'s work and the reason it succeeded. I do NOT think it succeeded because it was formerly a successful fanfic, and here's why: Fanfiction has already had an audience. Therefore, many of your potential fans have already read the story, and the rest of your potential fans know that they can find it online for free.
What you're doing when you re-publish a successful piece of fanfiction is putting it on the market and assuming that the same things that made it appeal to a fanbase will make it appeal to everybody. But fans of whatever it may be are a self-selecting group, and doesn't it seem likely that a lot of them will have already read the story?
Additionally, fanfiction and original fiction are not the same thing. Fanfiction relies on at least a passing knowledge of characters, themes, and setting. Fanfiction also tends to be written in a serial style with an emphasis on spending more time with your favorite characters v. tight plotting and action. It makes sense that different forms of storytelling would have different focuses, but one of these things is not like the other and there's no reason to assume this style will sell well on the mass market. (And no, Fifty Shades does not count as a reason - it is one example. That makes it an anomaly, not the norm.)
But wait! Authors say their P2P stories are reworked and edited so that they barely resemble their original forms. Okay, fine. I wonder how far you can take these stories from their original form without losing the very things that made them popular, but even if this is so...
What about legality?
Thus far, publishers have been acting under the "it's better to beg for forgiveness than ask for permission" principle. That's fine right up until it isn't. Stephenie Meyer may not be interested in suing anyone, but E.L. James herself has demanded fanfiction of her work be taken down, and many well-known authors like Anne McCaffrey have long stated that they don't allow fanfiction of their works in any form. Eventually, somebody is going to balk.
The courts may decide that P2P fanfiction is in fact legal. But publishers don't know that. They're walking on thin ice.
What it comes down to is just because something's salable doesn't make it legal, and just because something's legal doesn't make it salable. Either or both of these things may be true about pulled-to-publish fanfiction. But neither are proven. I don't think this is a good move by publishers, and I wonder what this says about their attitude toward the industry.