At its heart, it is a conflict of interest and a clear violation of traditional journalistic ethics. At the very least, it is contrary to what one might assume to be a societal norm. Once one is aware of what they're doing, one feels taken advantage of and that is simply not acceptable.
No, it's just not a good look for a news organization to have content so entangled with income, especially if they don't even mention it. I think http://thewirecutter.com/ does a good job, and they're also way more open about the fact that the site is covered in affiliate links.
They are almost assuredly added automatically so the author had no clue it was happening. I used to author a Wordpress plugin that did this for bloggers so they wouldn't need to worry about generating links through the Amazon website then going back to their Wordpress dashboard.