TL;DR: Because, physics.
Every once and a while Apple is accused of ignoring wireless charging on the iPhone, or stubbornly refusing to add it. Since the Apple Watch uses wireless charging exclusively, Apple is certainly doing neither in general. So, why isn’t it on iPhone in specific?
The Apple Watch has a glass or sapphire back which not only allows for the heart rate sensor but allows for the wireless charging. Wireless charging through glass or sapphire or plastic has been possible for a long, long time. Aluminum, which Apple switched to with the iPhone 5 in 2012, not so much.
Qualcomm announced technology to handle wireless charging on phones with metal casings, but only very, very recently—July 28, 2015, to be precise.
There are other consideration, of course, but when it comes to understanding why Apple hasn’t used wireless charging in iPhones to date, the existence of the right technologies is certainly a great place to start.