Farhad Manjoo says he's worried by the trend toward "native" advertising, where the ad is structured to "fit in" with the content of the website and often designed with the collaboration of a native advertising team that works with the publication. See this Land Rover spot at Slate for an example, and consider buying yourself a Land Rover while you do it—the finest British-made, Indian-owned cars around!
Except while I think Manjoo brings a lot of great facts to bear in his column about the ways in which native content can cause us to lower or psychological defense mechanisms against advertising, I don't think he's quite hit the right thing to worry about. If you want to know what to worry about, check out Erick Wemple's hit on Mike Allen and Playbook. I'm not totally convinced that Wemple has made his case here, but what Wemple is alleging is that not only does Allen put sponsored content in his daily emails (that's native advertising) he also slants his editorial coverage to be favorable to the messages of frequent sponsors.
It's the latter that you should worry about. Not the native ad for Land Rover in Slate, but the sentence in my editorial post where I in my own voice recommended Land Rovers.
Obviously native advertising relationships can induce these kind of ethical problems. But so can conventional advertising relationships. There's always been the risk that a newspaper isn't going to publish an exposé about the local department store when they know the store is their biggest advertiser. There's always been a strong taboo of journalistic ethics against this kind of thing, and Noam Chomsky's arguments that it's basically all a fraud have always had some force in my view. But whatever you make of these arguments, I would say this is one of the aspects of the media business that's changing the least thanks to technology. Writers and editors know who their sponsors are, and this may consciously or unconsciously bias their coverage—that's true with print ads, with TV ads, with banner ads, with "native" ads, with anything.