“How come?” is actually a very interesting phrase. It seems to have been an American invention of the 19th century, although similar forms date back several hundred years in English.
“How come?” is essentially synonymous with “why?”, but in popular usage it often serves a slightly different function. “How come?” carries a challenging, more emphatic tone than a simple “why?” would convey (”How come Jimmy never has to wash the dishes?”). Unlike “why,” “how come” strongly suggests that the questioner has already developed an opinion on the situation and has decided that something is not proper or fair.
Modern interpretation – Eminem: How come?
“How come” is actually an abbreviation of a longer phrase, which, although not known with certainty, was probably “how comes it” or “how does it come,” meaning “how did this (event, condition, etc.) happen to be this way.”