Could be the throw-out bearing. If the clutch does not have enough free-play in the pedal linkage, the throwout bearing will spin constantly, rather than only when you press the pedal. This will cause it to burn out quickly. It can also be casued by "riding" the clutch. You could try adjusting a little more free play into it, but it is likely toasted if it has been whining for a while.
Oh, and disregard Julio. His advice is for an automatic transmission, not manual.