The New York Post reported most of the complaints centered on the ads' overt sexual content.
"It was pulled because of some things that might be construed by some people to be offensive," said Metropolitan Transit Authority spokesman Tom Kelly.
The ad was for "Drawn Together," which is billed as "TV's first animated reality show." The series depicts cartoon characters having sex, high jinks and frat-house style debauchery while living together before cartoon "cameras," the Post said.
Richard Loomis, the Comedy Central's vice president of advertising and marketing, said making the ads as raunchy as possible was the responsible thing to do, so viewers would know the TV-MA-rated adult cartoon is not for children.