My bet is you got a bad alternator. Did it whine before you put the rebuilt alternator on? If not, then it's the alternator. Rebuilt doesn't mean what it used to any more.

Is the whine affected by engine speed rather than driving speed, and does turning on the headlights, heater blower, and all electrical accessories reduce the noise? Then it's the alternator. Have a car that did the same thing, and changing the alternator fixed the problem. It still always kept the battery charged though. Suspect a diode but never got around to finding out for sure.