I think there's a fine balance here - I think if you within a niche where you could very easily turn off readers by using affiliate links, you need to be more transparent with your use of them, i.e. make it painfully clear why you are using an affiliate link. To take this a step further, I think affiliate links within niche blogs should be representative of a true vote from the author. For example, I occasionally use affiliate links in my posts, but only for a handful of products that I actually sue myself and would publicly advocate.
I know for a fact that there are a lot of bloggers in the marketing space that will write posts JUST because a product has an affiliate program, or they will put together a post and then go hunt for all of the affiliate links - and while this may make some money, I think this is a example of how not to do affiliate marketing.
Just my $0.02.
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