Updated

The New York Times is being accused of having a double standard when it comes to questioning religion, after it ran an ad calling on Catholics to leave their church, but nixed an ad making the same plea to Muslims.

The newspaper published an ad from Wisconsin-based Freedom From Religion Foundation on March 9 which asked Catholics, “why send your children to parochial schools to be indoctrinated into the next generation of obedient donors and voters?” The ad went on to call loyalty to the faith misplaced “after two decades of sex scandals involving preying priests, church complicity, collusion and cover-up going all the way to the top.”

But in a story first reported by The Daily Caller, when Pamela Geller, a blogger and executive director of Stop Islamization of America, offered the same $39,000 for the Old Gray Lady to run an ad making a similar appeal to Muslims, the newspaper passed.

"This shows the hypocrisy of The New York Times, the "gold standard" in journalism, and its willingness to kowtow to violent Islamic supremacist intimidation," Geller told FoxNews.com.

Geller said her anti-Shariah ad was designed to mimic the anti-Catholic one. In calling on Muslims to quit their religion, the ad asked “Why put up with an institution that dehumanizes women and non-Muslims … [do] you keep identifying with the ideology that threatens liberty for women and menaces freedom by slaughtering, oppressing and subjugating non-Muslims… Join those of us who put humanity above the vengeful, hateful and violent teachings of Islam’s ‘prophet.’”

Times spokeswoman Eileen Murphy referred requests for comment to the letter the paper sent Geller when it declined to publish the ad.

"We have not made a decision not to publish the ad you refer to," stated the letter. "We made a decision to postpone publishing it in light of recent events in Afghanistan, including the Koran burning and the alleged killings of Afghani civilians by a member of the U.S. military.  It is our belief that fallout from running this ad now could put US troops and civilians in the region in danger and we would like to avoid that."

Bill Donohue, the president of the Catholic League, called the first ad “vile.” But he said running it was a “judgment call.” However, the decision not to run Geller’s ad shows an agenda, he told FoxNews.com.

“It shows the disparate treatment and the duplicity of The New York Times,” Donohue said. “You can trash some religions, like Roman Catholicism, with impunity, but you cannot trash Islam?”