A lot of magazines sell sponsored content to advertisers. (Business Insider has several sponsored content series running right now, for instance.) The usual rule is that such stories must be clearly labeled so that readers can see whether editorial may have been influenced by advertisers. Normally, however, both the publisher and the advertiser try to make the content credible or useful in some way, because readers can spot blatant propaganda a mile away -- and that's of no use to anyone.
Blatant propaganda, however, is exactly what The Atlantic appears to have published. The article, titled "David Miscavige Leads Scientology to Milestone Year," was an encomium to the the "ecclesiastical" leader of the church and his many accomplishments (which mostly include buying old buildings and turning them into new churches, according to the article).
The Atlantic is a highbrow magazine known for it famous writers and agenda-shaping journalism. This, decidedly, was not it.
Almost as soon as the piece was published, it was taken down and replaced by this corrective note:
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