On his radio show on Friday, Mayor Michael Bloomberg defended a court decision forcing the MTA to display an ad equating Muslim radicals with savages.
A federal judge on Thursday sided with the conservative blogger behind the ad, who sued the MTA for refusing to run it.
The MTA said the ads violated its defamation policy.
Mayor Bloomberg said the blogger is protected by the First Amendment, a right he said that Americans are fortunate to have.
"We have a very different view of the world and we've grown up in a different culture where we have a freedom of expression that other people don't and a tolerance other people don't," the mayor said. said.
The ad will run in 10 subway stations starting next week.