The entry level, 16gb iPhone has a profit margin that is bigger than average, but not huge. The 64gb iPhone on the other hand.. it's like printing money. The markup doesn't even begin to compare to what the bigger storage actually cost to Apple. Apple makes a LOOOOT of money out of the customers who have bigger needs than average.
That's been Apple's strategy forever, people who want more have to pay a lot more than what it's really worth. I can remember the entry level iBook (during the PPC days) being sold with goddamn combo DVD reader/CD writer drives in a time where EVERY SINGLE PC LAPTOP SOLD, even the cheapest crap, had a DVD writer. Just to push people onto the higher profit margin.
I love Apple products but they really know how to milk their customers dry. Hacker News's audience wouldn't fall for that, but I can remember the markup on ram, when they still sold devices with 1 or 2gb of ram when the competition had 4gb on their cheapest stuff, with huge markups on the online apple store if you ordered a laptop with more ram. People here know how to put more ram in their computers and know not to order a macbook with "Apple's ram" (... a traditional thing that is going to die with the retina mbp and its soldered ram), but the average joe just got ripped off hardcore.
If you only look at their entry products, like the 16gb iPhone, the 21" iMac, the 11" MBA, yeah, Apple seems reasonable. Any other Apple product ? the margins on those things is something no one else could pull off without getting lynched.