Bleeding Cool reported late last week (and B&N confirmed today) that Marvel will no longer be distributing the weekly comic books to B&N stores. B&N hasn't given a reason for the change, but they did note that they will still be carrying the longer and more expensive graphic novels:
This is a Marvel decision to pull single issue comics from retailers. Not a B&N decision. This doesn't apply to graphic novels.
Marvel is unavailable for comment at this time, so there's no way to know exactly why they made this decision nor whether it represents a major shift in their distribution plans.
Update: Marvel responded to PW with the news that Marvel had ended their relationship with BAM and B&N close to 3 months ago, with little fanfare. In fact, Marvel pulled out of all bookstores this Fall, not just the 2 biggies in the US.
But while I cannot speak for Marvel, I can add that Marvel does not appear to have pulled back from distributing to comic book stores. ComiXology is still showing that comic book buyers can still add Marvel titles to their pull lists for this week, next week, and the week after. This tells me that comiXology still expects the comics to be available at their partner comic shops.
TBH I was half afraid that the B&N news was the first sign that Marvel was abandoning floppies entirely. That sounds crazy, I know, but that doesn't mean that Marvel couldn't have found a compelling justification for taking their weekly comic releases digital- only - but that's not the case.
Now that Marvel has pulled out of bookstores they're going to have to depend more heavily on digital sales and on sales via comics shops, but I don't think they're going to feel much of a pinch. In my area there were only a couple B&N stores within driving distance, but according to comiXology's shop locator there were 50 comic book stores within 50 miles. Even if I exclude the ones on the other side of the Chesapeake Bay and the stores in Gainsville or Annapolis, I still have some dozens and dozens of places to buy comic books.
Of course, not everyone is as lucky to live in suburbia as I am, but then again there are places in the US where B&N's 600 or so stores are pretty thin on the ground as well.