I belive Apu is of Indian origin. The Indians, in general, are not exactly fond of Muslims, especially Pakistanis, but Muslims in general. Muslims conquered India, once upon a time, and ruled with an Iron fist for centuries. Indians are apparently taught all this in their schools, just as we were once taught about the Bad Old Brits. (They learn about the Bad Old Brits too of course, although their military customs, ranks, uniforms, etc, still follow the British model).
The owner of the Quick-E-Mart is a Pakistani sleeper agent, and OJ Simpson will not rest until he prooves it,