This was a terrible article. The complaints have nothing to do with the buy box. I can think of three ways that "publishers aren't getting paid" could be true:

1) Books are stolen

2) Books are counterfeit

3) Books were purchased through "unauthorized" channels, e.g. free review copies

None of these is a problem with the Amazon buy box. We don't complain that "Samsung doesn't get paid when people buy Samsing TVs at Best Buy" and I don't see how this is any different.

I think Amazon is guilty of a lot of shady practices that harm businesses (like co-mingling potentially counterfeit Fulfillment by Amazon inventory with Ships From and Sold by Amazon.com inventory). But this article makes no sense.