This will ruffle a feather or two in the Muslim community... er... wait... what's that?
Oh. It's an anti-Catholic ad you say?
Well then, never mind.
It's not the first time the New York Times has run an FFRF ad attacking the Catholic Church so we shouldn't be surprised particularly when they do in fact reject certain other anti-religion ads.
The Times, your paper of record for anti-Catholic screeds.