"Native advertising" is all about deception. Even if, at some level, you understand they weren't put together by the magazine's staff, you're still expected to see them as partaking of the magazine's trustworthiness.
The Atlantic is a venerated magazine, which has been celebrated for the way it has made use of the Internet probably better than any highbrow publication. But taking paid puff pieces from Scientology? This innovation is resulting in a big backlash.