There is absolutely no reason to ever even conceive of flying it again.
SpaceShipOne was unsafe1, barely met its requirements2 (which was certainly good enough) and was designed specifically and solely to win the prize.
The tiny crew compartment meant that there was zero incentive to certify it for passengers; it would certainly have not been economic for tourist flights.
I wouldn't call it a prototype since it was designed to meet certain requirements, met them, and was retired before it killed anybody.
1 "SpaceShipOne had lost control. It spiraled up, making twenty-nine rotations."
2 "To solve the problem that SpaceShipOne barely reached space even when much lighter than it would have been for an Ansari X Prize attempt..."
Source: Burt Rutan's Race to Space, Dan Linehan, 2011