Ask HN: Considering an affiliate program. How to decide/implement?

We're considering an affiliate program for one of our web apps. Something along the lines of what Freshbooks and 37signals does.

My only concern is this: we have a really good reputation online and serve a niche market. If we have an affiliate program, I fear people would be more skeptical of the referral ("you're just referring them because you get a cut").

Is this a valid fear?

Any thoughts on affiliate programs or how to best implement them?