I once created a project based on affiliate links and I researched the implications of this a lot.
I came to the conclusion for a corporate project it's a very elegant way to make money, as theoretically it's a win-win for everone involved.
But there is one big problem, especially for smaller projects where the people who write the content also manage the website: Subconciously you start identifying with the products you recommend.
It's easy to lie to yourself. Like one guy on the github thread, suggesting
> "Another benefit of more income from affiliate: We could fund small privacy open source software / service projects in form of donations, too.
If the project would be able to even fund other projects with running on affiliate money, then it would also be possible to live off donation or a shop and simply focus on your own project.
There is only one way of having a project that sides with the users: Actually getting the money directly from the users.
With affiliate links the products you recommend become your customers, so you start to become accountable towards them, and the users become your product.
This happens slowly over time and mostly subconsciously. At first everything seems to be ok, but at one point all the relevant questions resolve around how to please the affiliate customers.