A burrito costing $1 to make but Chipotle charging $6 for it is like saying the 16GB iPhone costs Apple $20 to make, but they charge $200 for it... which is true. If I want to add storage to my iPhone, the price skyrockets.
No, it very much is not true. They sell that 16GB iPhone for $649. You may only pay $200 up front, but your carrier is paying the extra $450 if you aren't. I think you're thinking of it as a 50% price increase from 16GB to 32GB and 100% increase from 16GB to 64GB. It is not. The price increases are 15% and 30%, respectively.
However, if I want to add cheese to my burrito at Chipotle, the price isn't going up.
At McDonalds an extra slice of American cheese on your McDouble will cost you $.59, a 59% price increase.