To be clear, the 5% are actually coming out of Apple's pocket, not the developer's. Which, I suppose, is an argument for the service. Also, (though I'm not completely sure) it's 5% of anything bought from the store, not just said app, until that affiliate token is overwritten by another one. So that could potentially be a big chunk of commissions.

Overall, I'm thinking "why not? it's not hurting anybody", but I just feel like they're the agent that screws their clients on how much they're really getting paid. (or to be more Apple-centric: Jobs only giving a small chunk of what Atari paid him to Woz for Woz's work)

However, I don't follow you with "there are 10 more websites doing very similar stuff". It's not a justification to me.