We've put a fair bit of thought into how to structure this project to minimise or negate the chance that at some point down the road Amazon decides they don't want Charity Science as an affiliate, as people have discussed in comments. This does seem to be the most plausible downside, though we think that it makes sense to deal with it if and when it arises and it likely wouldn't be that bad. Given that other individuals and non-profits have promoted similar affiliate links, often presented as a way to support them or their charity, it is improbable. Nonetheless to make it clear that we're directing fresh sales to Amazon, we've redone the 'Shop for Charity' page to feature a bookstore with selected books relevant to EA. You can see the new copy there, which is well within the space that Amazon has allowed in the past (we haven't changed this post to keep the comments making sense, and it'll be off the Forum front page soon, with the Shop for Charity page itself what people link to in future).
Charity Science does have an advantage in running an affiliate account as the commission goes to it (as Amazon intends), and only gets passed through to other charities because all unrestricted money going to us does, as a matter of policy. So it's not like we're an individual saying "If you buy through me I'll donate some money to charity"; it's a standard case of the money going to the entity that has the affiliate account.

Update: I've been accepted to the German affiliates program! Ich hoffe dass dies viel Geld für einige der besten Wohltätigkeitsorganisationen der Welt zu erhöhen.
And I've now extended this to Austria, which appears to also run off Amazon.de - any Austrians can correct me if I'm wrong.
When shopping via this link, I see no indication of a commission going to you. Could you confirm that this is still working?
Yes, I can confirm that - there's simply no visual feedback that it's worked, but once you visit Amazon via one of our links any purchases you make in that shopping session get 5% commission.