It's just that their business model -- charging per GB, instead of per GB of new data that nobody else is storing yet -- leaves them susceptible to arbitrage. I.e. customers can steal the economies of scale if they collaborate.
You know how Starbucks charges $5 for a small and $6 for a large? It's the same thing. If two people want smalls, but collaborate, they can just split a large and save $2 each. It's the same idea, except that arbitrage becomes more realistic when it's electronic.
(I've ignored compression in the whole discussion for simplicity. If AWS wants a business model that isn't arbitragable based on compression they would have to charge based on how compressable your data is. Also, next generation compression algorithms -- another blog post on that later perhaps -- could achieve compression rates that have the same economies of cross-customer scale that data deduplication does, so really it would have to be price based on how compressable your data is __given all of the other data S3 is storing__.)
(EDIT: made starbucks example simpler.)