I’m not sure where’s the problem with affiliate links and why people hate them. It’s like when they see something like ?aff123 or #abcd123 or similar affiliate tracking in the end of url they think it’s something wrong with it, or maybe it’s some sort of scam. Hell, even I have been in that situation and thinking the same thing. Maybe it is in human nature to avoid such things, I don’t know, but it really intrigues me.
Probably because of those reasons, to trick the readers mind and to keep them calm, marketers have been cloaking or redirecting their affiliate links for a long time now (and also to protect their affiliate links from getting hijacked). It was a lot complicated back then, there were many ways of redirecting the links (like .htaccess redirection, which was really pain in the butt), but luckily things have change.