Chris Foresman writes for ArsTechnica about the negotiations between Apple and magazine publishers over how to sell subscriptions.
Someone has to have the subscriber information if only to validate a credit card. But who owns the list of subscribers? Publishers (and many other organizations) treat their customer lists as gold. That's why sales through the App Store cause a problem: it's Apple, not the publisher, who winds up with the customer list.
This discussion has been proceeding for quite some time now, and it appears that it will continue for a long time to come.
As with iBooks, it's the big guys who are talking. Small presses and small magazines seem to be out of the picture. Perhaps, they'll use their small size to come up with an elegant way around these hurdles. It would be very web-like to use the technology to level the big/small playing field.