The simple matter is that there are people who need the charger either because they don't have one, or they don't know/care about charger/cable specs to find out which one works for the Apple device they're buying and hence simply needs to "buy an iPhone with the right charger" to get on with their lives. Or they just want one more of the right one they already have so that they can charge devices simultaneously.
I don't think Apple at present accounts for such consumers and this is where the problem lies. I've had many friends buy the iPhone, separately buy chargers for cheap and wonder why it's charging slow even though "it fits". Having an option to buy an iPhone that has these included in the box solves such issues.