Rutan is doing it because he wants to prove that it doesn't take a government agency to get into orbit and that it could be economically feasible. He has mentioned this a few times in interviews. The X-Prize would just be a nice bonus.
Scaled Composites is taking a step by step approach to this, much like NASA and the Soviets did. While SpaceShipOne won't be able to attain orbit, the next generation might be able to. They are developing the technology to apply to the next generation, so some will transfer but we will have to wait and see how much. The first American in space didn't achieve orbit either.
After this prize is won, I am sure there will be a new prize for the first to achieve orbit, much like the challenges given to early pilots for crossing the Atlantic etc. kept getting harder.
The day I would love to see is the day when we have true space craft, not craft that are little more than ballistic projectiles. Something like what you see in Star Trek or Babylon 5 (I could do without the faster than light part).
goates