Parts markup is just simply how it works in the industry though. That's how it's been and it's not going away. I do agree that the shop in question is a bit on the high end, but I'm sure that price was agreed upon before any work was done. Nobody was forced to pay those prices, they could have shopped around and taken their business elsewhere.
Again, there is a lot of expenses that go along with running a good repair business. These people aren't getting rich off of the parts markup, it's just getting put right back into business expenses. The places that really do screw the customers, yeah there's a lot out there, but they won't be in business very long.