Average Apple Genius salary seems to be around $21 an hour. Therefore it's very conceivable that their hourly repair rate is at least triple that: $63 an hour. Then there's the cost that any repair might potentially cause more issues, you got the costs of running the store in general, lighting, heating etc.
After running a business myself I can promise you that, until you see it for yourself, you are oblivious to all the hidden costs that quickly mount up into a charged rate.
Since when did any copany have to act like a charity when it came to out of warranty repair costs? There's many companies that expect you to return items back at your expense in the correct packaging AND pay for the return shipping, even to have something repaired under warranty.
Quite acting like this is somehow unique to Apple. I gave up with getting my Onkyo Receiver repaired under warranty because it would have cost me over $100 to have it shipped there and back just so they could reflash the firmware on it.