The Atlantic is really, really, really, really, really, really, really, really sorry about that Scientology ad. From an email sent out this morning:

We screwed up. It shouldn’t have taken a wave of constructive criticism — but it has — to alert us that we’ve made a mistake, possibly several mistakes. We now realize that as we explored new forms of digital advertising, we failed to update the policies that must govern the decisions we make along the way.  It’s safe to say that we are thinking a lot more about these policies after running this ad than we did beforehand. In the meantime, we have decided to withdraw the ad until we figure all of this out.  We remain committed to and enthusiastic about innovation in digital advertising, but acknowledge—sheepishly—that that we got ahead of ourselves.  We are sorry, and we’re working very hard to put things right.   

If you remember correctly, the ad was something of a spectacle. Fun to look at though.