With advertisers set to pour more and more money into native ads, 2013 could be a great year for well-positioned publishers.

But publishers looking at native ads as a solution to ad blockers and paltry display CPMs should tread carefully.

Native ads aren’t a panacea and the premiums advertisers may be willing to pay for them shouldn’t distract from the fact that native ads can be risky ads.

That’s a lesson that The Atlantic learned the hard way after it published an advertorial from the controversial religious organization Scientology.

The advertorial bearing the headline, David Miscavige Leads Scientology to Milestone Year, is a chronicle of the growth of the organization in 2012 from, of course, the perspective of the organization.

Accompanied by photos showing the dedication of new Scientology churches, the advertorial is clearly marked as “Sponsor Content” with an explanation that:

Sponsored Content is created by The Atlantic’s Promotions Department in partnership with our advertisers. The Atlantic editorial team is not involved in the creation of this content.

Oops, somebody saw your ad!

While prominently marked as sponsored content, it didn’t take long for the internet to notice. Within hours, the advertorial was making the rounds on Twitter, Facebook and other social hubs.

The Atlantic’s first response to the attention being focused on the advertorial: moderate comments. But that apparently didn’t work and the page was eventually pulled. In its place, The Atlantic posted a message, “We have temporarily suspended this advertising campaign pending a review of our policies that govern sponsor content and subsequent comment threads.”

Which begs the question: what was there to review? The Atlantic is a savvy digital publisher, and the company’s “Promotions Department” must have known that Scientology is a controversial organization before it accepted the organization’s money.

Based on a screenshot of the page in question, it’s safe to say that the sponsored content was professionally created and time taken to prepare it for publication. In other words, it’s inconceivable that The Atlantic hadn’t reviewed the advertorial before it went live. The real problem: the internet noticed it.

With this in mind, The Atlantic’s message might as well have been “We have permanently removed this advertising campaign because you actually noticed it.”

Native ads: where advertisers meet the undercarriage of a bus?

Once discovered, The Atlantic apparently wasn’t prepared to stick by its advertiser and decided to introduce Scientology to the underside of a bus. Which, regardless of one’s personal opinion about Scientology, should be of concern, particularly to those with high hopes for the burgeoning native ad market.

While it’s easy to dismiss the incident in question as a poor example given the fact that Scientology is a lighting rod, there is a fundamental question advertisers must ask themselves: do the publishers we’re paying a premium to for native ad experiences have the stomach to stand by us if their audiences react negatively to sponsored content?

The demand for native ads is creating interesting opportunities for publishers, but those publishers shouldn’t be so quick to accept native ad dollars before evaluating their comfort with the advertiser and content. And when they do take an advertiser’s money, they should have the wherewithal hold up their end of the bargain.