Pamela Geller, who leads an organization called Stop Islamization of America, said the ads were meant to help provide resources for Muslims who are fearful of leaving the faith.
"It's not offensive to Muslims, it's religious freedom," she said. "It's not targeted at practicing Muslims. It doesn't say 'leave,' it says 'leaving' with a question mark."
Geller said the ad buy cost about $8,000, contributed by the readers of her blog, Atlas Shrugs, and other websites. Similar ads have run on buses in Miami, and she said ad buys were planned for other cities.
Metropolitan Transportation Authority officials said Geller's ad was reviewed and did not violate the agency's guidelines.
"The religion in question would not change the determination that the language in the ad does not violate guidelines," MTA spokesman Kevin Ortiz said Wednesday.
All ads are screened, MTA spokesman Aaron Donovan said. Most are reviewed by the company that handles the MTA's advertising opportunities, but some are sent to the MTA for ultimate approval.
Last month, Miami-Dade Transit pulled the ads from 10 buses after deciding they "may be offensive to Islam," according to The Miami Herald. But the agency decided to reinstall them after reviewing the ads with the county attorney's office.
The county decided "although they may be considered offensive by some, they do not fall under the general guidelines that would warrant their removal," Transit spokesman Clinton Forbes told the newspaper.
Glenn Smith, a professor at California Western School of Law in San Diego, said discriminating against the ads could result in First Amendment issues for the city.
While people may find the content objectionable, courts have ruled that the First Amendment requires Americans to put up with "a lot of unenlightened and objectionable messages," he said.
"It's sort of the price of keeping government out of the marketplace of ideas," he said.
Eugene Volokh, a First Amendment expert at UCLA School of Law, said the ads could leave some Muslims reluctant to ride the bus. There could also be a risk that some extremist groups might bomb the buses, although that possibility wouldn't limit free speech rights, he said.
The agency had received no complaints since the ads went up on May 14, MTA spokesman Aaron Donovan said. The 30 or so buses with the ads pass through all five boroughs of the city.
Council member Robert Jackson, a Muslim, said he had not seen the ad. But he questioned the criteria the MTA uses in determining what is appropriate.
He also takes issue with the content. He doesn't believe anyone is being forced to stay in a religion, especially in America, which was built on religious freedom.
"I think this is a campaign by the extreme right, those that are against the Muslim religion," he said. "Quite frankly, I would think the average New Yorker would take it for what it's worth."
Faiza Ali, of the New York chapter of the Council on American-Islamic Relations, said the ads were based on a false premise that people face coercion to remain with Islam. She said Muslims believe faith that is forced is not true belief.
"Geller is free to say what she likes just as concerned community members are free to criticize her motives," Ali said.
Geller has a history of speaking out against Muslims, and the ads are "a smoke screen to advance her long-standing history of anti-Muslim bigotry," Ali said.
Geller said she had no problem with Muslims, but was working to "maintain the separation of mosque and state." She is also among those speaking out against the building of a mosque and cultural center near ground zero.