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There's probably only 80 different commercial airplane models. This testing probably costs around $1000/hr - figure 5 days testing @ 8 hours a day = 3200 hours = 3.2 million dollars. Seems to be a reasonable price to pay.

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As I said, it's not just the different models, it's the different avionics suites within each model (e.g. two aircraft of the same model might have different radios or different navigation equipment, etc.). For each plane, you would need a few hours of testing, which probably costs more than $1000/hour: you have to pay for the plane, the crew (who have to be qualified to perform this type of testing), the ground support equipment, maintenance support, and any fuel burned during testing (e.g. running the APU to provide power during testing will consume a small but not insignificant quantity of fuel).

EDIT: Almost forgot: After the testing is complete, you have to pay to have a test report written up and published, and then you have to pay for the FAA certification process. Probably not cheap.

The US Treasury has less cash on hand than Apple. Apple makes prepayments of a billion dollars for parts. The numbers you're tossing around are, in context, very cheap.

Apple only pays for things that they expect good ROI for. I doubt very highly if they would recoup the money spent to get their phones FAA-certified, let alone the opportunity costs compared to spending that money on something else.

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