How Come

The oldest reference for "how come" in the Oxford English Dictionary (OED) is an entry in Bartlett's Dictionary of Americanisms published in 1848. The OED calls "how come" an American coinage, but the entry in Bartlett's indicates it originated in England: "Doubtless an English phrase, brought over by the original settlers." "How come" is believed to be a shortened from "how did it come about that," or "how comes it, then"  It makes sense, but has somehow been lost in current usage and many people do not really know what it means, but use it anyway. That phrase bugs me. How come people say how come instead of why?