It's an affiliate program similar to Amazon's. The retailer registers with Comixology, gives his "digital storefront" address to his customers, and gets a cut of the profits off the sales in their "store".
Sorry to be dense, but I still don't get it. But I'll try:
Say the website for my local LCS lists new arrivals every week (which it does; they even post it on their Facebook page to alert me). From now on, every title on the list would be a hot link to the actual download, and they would get a percentage of the sale? That's all well and fine, except that I can go to any other LCS' website anywhere in the US and see the same information and give them the money. The thing that keeps me from going to Midtown Comics or Forbidden Planet as opposed to my decidedly more modest LCS is the day-long drive to NYC, but with the internet that's not an issue. For that matter, I can go to Diamond's site and see the list there. So the only thing putting money in the pocket of the LCS is the loyalty and generosity of its customers, who could just as easily do an end-run around them (whereas today their "loyalty" is based at least partially on physical location).
Maybe, the LCS doesn't have something in stock that the customer wants and Comixology does. Instead of waiting for the order to ship, they can have the product the same day, and still support the LCS while doing so. Sure, there's not a huge ton of money involved in this, but atleast the shop will get something.
So I guess the goal for each LCS in the future will be to design the site that draws the most customers, so they'll follow your links and not the other guys'. Which means just as today the bricks and mortar store has to branch out to RPGs, DVDs and so on to "out-cool" the competition, the "shops" of the future will be websites with Flash-based games, breaking news, art and such stuff as appeals to web surfers.
Local World of Warcraft groups (guilds?) have their own blogs, Facebooks, message boards, etc even though WoW is a global game.
Unless they make this the ONLY way to download comics, I can't see it being much help to many shop owners. And assuming they also make it possible to download from Barnes and Noble and other major booksellers (and they'd be crazy not to), it seems pretty certain most of the business will go those guys, who have much higher-profile web presences and names that engender more customer confidence than say, "The Android Dungeon".
I don't know, but customer loyalty goes a long way. I've seen local music shops survive even with major retailers coming to the area and the advent of iTunes. The digital comics market is still very new and it's going to take a few years before everything settles.