The episode that aired that night depicted the filmmakers sodomizing Indiana Jones, the character played by Harrison Ford. Critics have accused Steven Spielberg and George Lucas of desecrating beloved films and franchises by reworking them to remove politically incorrect items (no more guns in "E.T."), and adding content (more alien creatures in "Star Wars").
Some people thought that portraying Spielberg and Lucas as rapists was one joke gone too far. New York's Daily News located a number of people who objected to the use of rape as a cartoon punchline and also thought the scheduling of the episode on Yom Kippur was anti-Semitic.
According to Nikki Finke's Deadline Hollywood site, executives at Paramount, which owns Comedy Central, weren't too upset about the portrayal of two of Hollywood's biggest stars as backwoods yokel rapists, primarily because they hadn't seen the episode.
Oh yeah, the episode was actually about Cartman's Sino-phobic view of the Chinese and was filled with ethnic Chinese stereotypes. The title was "The Chinese Probrem."