Here's the list I was referring to, this is just the list of independent bookstores that are selling the Kobo.
http://www.indiebound.org/ebooks
The home page has a link where you can search for all independent bookstores in your area, not just those that sell the Kobo. The problem isn't that Kobo only sells to a few independent bookstores, it's that only a few independent bookstores signed up to participate in the Kobo program.
The bookstore I got mine from explained to me that they don't make a whole lot of money on the Kobo program, but it has brought more customers into the store, me for instance. I had never heard of the store until I started doing research to find a Kobo Glo. Apparently I was not the only one and they have now sold several. I've returned to that store a time or two and purchased things there. The owner remembers me because of my emails asking about the Kobo and refers to me as "The Kobo Guy"!
They had decent brand exposure through Borders when that was still around, it's how I got my first Kobo. When Borders disappeared they were left without a way to really continue in the US market and decided to create the independent bookstore program. Will it work? Only time will tell, I do know it worked for me.