Earlier this week Gawker’s Hamilton Nolan wrote that Rolling Stone has little hope of capitalizing on the notoriety of Michael Hastings’ profile of Gen. Stanley McChrystal to increase newsstand sales and drive more subscriptions. As Nolan writes, “[w]hereas once people would have rushed out to newsstands to pick up copies of Rolling Stone and read what all fuss was about with McChrystal, now they either A) read that one single story on RS’s website, for free, or B) read it at the competition’s website for free, which is what happened in this case.” (Rolling Stone’s inability to get its own story online in a timely fashion remains frankly mind-boggling.)

Nolan argues that Rolling Stone, Esquire and Vanity Fair put out stories as good as those found in The New Yorker or The Atlantic, but magazines in the former group aren’t taken seriously as a whole because their good stuff is mixed in with so much fluff. He calls this “Good Stories, Bad Magazine Syndrome,” and laments that Rolling Stone and other sufferers “will never put out enough of those stories to make the types of people who care about those stories seriously consider reading the magazine on a regular basis.”

Good point, but Nolan isn’t really talking about the puzzle of how you brand a combination of get-everybody-talking journalism and cotton-candy features. He’s discussing a much larger problem:

Everyone knows that you don’t need to subscribe to Rolling Stone in order to read the five great stories they publish every year; just wait until you hear those stories mentioned elsewhere and check in then…The internet has split each and every story from every outlet into its own discrete item. Unless your publication is consistent enough to somehow pull all of these separate links into a coherent whole, you’ll never be a destination, per se. You’re just hosting writers and writing checks.

Nolan comes face-to-face with that problem, but I think he blinked. Because what if consistency isn’t enough? What happens to news organizations as we know them if this atomization of content is so thorough and irreversible that no publication can pull its discrete articles into a coherent whole? Without coherent brands, will any publication host writers and write checks?

In the months after I went freelance, I talked with a few organizations about potential newsroom jobs. During the first couple such conversations, I apologized for having read plenty of articles from Publication X without being familiar with its site, explaining that I mostly read individual articles that found their way to me. Later, I quit apologizing — because this is increasingly the reality of how more and more of us read. Among general-interest publications, I read The Atlantic and The New Yorker because they still show up at the house in print. I skim The New York Times because it’s the closest thing I have to a hometown paper, which is either nostalgia or dangerously close to it. For me, every other brand has been blown to fragments that arrive sifted by Twitter and Facebook, or are turned up by search. The future may belong to “bottom-up” brands designed to be encountered in bits and pieces — the home pages of companies such as Demand Media, About.com and YouTube are rarely glimpsed and for all intents and purposes irrelevant.

As the fragmentation of content continues, the importance of traditional brands’ section pages and home pages will continue to wane — which newsroom middle managers will find a lot more frightening than readers will. Section and home pages aggregate news for readers, yes, but readers are increasingly doing that themselves through personalization, or trusting their peers to do it for them. Too often, home pages are committee-built disasters anyway — a cacophony of news, features and corporate messaging from every internal constituency too big to be ignored. Readers, relentlessly trained to hunt for signal, rightly dismiss them as noise. When he was consulting for the Guardian, TBD.com’s Jim Brady shut down the Guardian America front page, explaining to PaidContent’s David Kaplan that “you’re better off putting your stories on Twitter and posting them on Digg and Facebook and pitching them to blogs that can move a lot of traffic, than posting them on a section front that’s getting no traffic anyway. One of the things I pushed for was that you have to get away from the idea of getting people to simply come to your home page. You have to get your home page to the people.”

If destination sites crumble, how do the bills get paid? I believe that people will pay for content [disclosure: I’m a consultant for Journalism Online], but paywalls and meters limited to a single site may be short-term solutions, because they’re ideas that spring from the old model of large brands and destination sites. Ultimately, what we may need is not paywalls but paytags — bits of code that accompany individual articles or features, and that allow them to be paid for. MTV’s Maya Baratz is ahead of the curve here, urging publishers to think of their products not as platforms, but as apps — which to Baratz means “not only allowing, but thriving off of, having your content live elsewhere.” But between wallet friction and the penny gap, the mechanics of paytags make paywalls and single-site meters look like comparatively simple problems to solve.

As readers, we understand that publications have been atomized — our own habits increasingly show us that every day. But publishers need to face the consequences of what that means. And that won’t be easy: Their entire world, from planning to production to distribution to promotion to how to get people to pay for it, is built around a fundamentally different set of organizing principles. What if those organizing principles are already obsolete?