that's the fee.
Which granted, over millions and millions of devices, is NOT chump change.
But remember that Apple makes a ton of revenue, 233 billion in 2015. So much so they lost 5 billion dollars last year on fluctuations in the foreign currency exchange market(which might be an outlier here, because 2015 was a fucked up year but with Brexit, 2016 might still also be a weirder fluctuation).
So if you look at the raw numbers, in order to even make their revenues push up by 1%, they'd have to sell something like over half a billion headphones and charger docks and whatever else uses lightning. That's one lightning device for every two or three people in the US, Canada, Mexico and Europe. Every adult, every child, everyone young, everyone old, and everyone in between.
It's not revenue. They're also giving you a 3.5mm adapter for anything that you have laying around that isn't lightning enabled already, with replacements costing 9 dollars.