The ad was paid for by the American Freedom Defense Initiative, an organization that opposes radical Islamic influence in the United States. The group's executive director says she doesn't find the advertisement offensive.
The group sued the Metropolitan Transportation Authority to demand it accept the advertisement, which was approved Monday.
MTA spokesman Kevin Ortiz says the agency doesn't endorse the advertisement's views.
The plan for a mosque just blocks from the World Trade Center site has ignited a national debate about the limits of tolerance and the symbolism of ground zero.