Yeah, GM paid back the $X-billion government loan, but they still have that $XX-billion from the government still invested in it... (I don't know the exact figures off-hand)
...granted, if GM stays on the straight and narrow, keeps moving forward with their strict build quality and reliability guidelines, exciting product, and proper firm-handing management of the unions, they may improve themselves to the point where they can pay back ALL of the government investment when they go public again...
The government's stance all along has been that it will sell all of its shares on the open market when GM goes public again... hell, the government may actually profit from all of this.