They definitely have their own inventory. Things like cereal and diapers ship in completely purple jet.com boxes (http://i.imgur.com/WUisXzH.jpg). It's only more obscure stuff that ships from other retailers.
I think the idea is that they want to have a long tail of inventory and are willing to take a loss on those items for now, but for high-volume items they are already doing them in-house.
Jet has warehouses to cover the whole U.S. With two day shipping on core items. As well as a marketplace like the other businesses you mentioned.
Jet is giving its customers all the commission they would have made, all of the supply chain savings they can get out of not having physical stores, paying with certain credit cards like Costco does, as well as any other savings the technology can squeeze out. They are giving all of that back to the customer.
For the Affiliate portion of their business they are giving jet cash to customers. That is a small portion of their business 15%, they are doing that as a value add for people who pay for the membership.
At the risk of pasting the entire content of the article here...
>Many of the companies whose brands were removed from the Jet Anywhere program appeared to be unaware that they were listed on the site when contacted by The Wall Street Journal.
>Spokespeople for Wal-Mart, Walgreens, Target Corp., Staples Inc., and Estée Lauder Cos.—who all had their links removed from Jet Anywhere—said Jet isn’t a partner.
>A spokeswoman for skin care company Kiehl’s, a unit of L’Oréal, said Kiehl’s had “requested to end the direct affiliate relationship as procedures outlined in our current affiliate program weren't being followed.”
>Online fashion marketplace Bluefly Inc. was surprised to see its brand had been added to Jet Anywhere, said Chief Marketing Officer Carly Rosenberg, a program Bluefly was never told about even though it had been in discussions with Jet since last year to sell products directly on its site. “I felt a little blindsided by it,” said Ms. Rosenberg, “I just think they went about it the wrong way.”
Yes, Jet has their own retail operation, but they are also breaking the terms of many affiliate programs with "Jet Anywhere" by paying people to use affiliate links.