All parts are marked up for resale reletive to what what the SHOP paid for them. You did not buy your parts from napa , they did. And if they paid to napa the same price you could have they still will mark it up. Basic business practice.
Ford parts are marked up to reflect a 40% Retained Gross Profit and when outside parts are procured they are marked up only 30% r.g.p.
I don't know what business you're in nor how you make profit for your paycheck, but even if the dollars spent are high, no one stays in business at 0% retained profit.
DO NOT attempt to rebut that you could have got them for less elsewhere. You didn't ! If that's where you wish to get your car repaired then go there, it's a free enterprise country. At the end of the day , mechanics cannot go to the grocery store nor pay their rent with a hand shake and a pat on the back.