My personal opinion based on what information he gave, I don't think he was ripped off. They might be higher than other shops, but that is why you get an estimate before you agree to let them do the work. The estimate should show you EXACTLY what it is going to cost and what they are going to do. If there is any other work to be done other than what they quoted, they should contact you BEFORE doing any more work.
If OP just dropped it off and didn't go through the contract, that is on him. Not the shop.
Like I said, I am only going off what information he included. From what he said, it doesn't sound like they did a bunch of extra work.
To reiterate, yes there is a mark up on parts. Some more than others. For example: I distribute cabinets for a living. It is a business that I have been co owner of for over 7 years now. Depending on if it is walk in, contractors, or dealers, our mark up varies. For walk in, because they are a huge pain in the @$$, our mark up is 75% of wholesale. That is still easy 50% less than what you get them for at home depot or the like and almost 80% less than what you pay at a custom cabinet shop.
If we didn't mark up prices, we wouldn't still be in business. It's called making a profit to meet extra expenses.