Lets do some math.
For FY2014 -
Apple Revenue - $183 billion
Apple Profit - $39 billion
Profit margin - 21.3%
iPhone revenue was $100 billion last year
So lets say iPhone has 30% profit margin.
$100 billion x 30% profit margin = $30 billion profit
That leaves only $9 billion in profit for the rest of the company.
That leaves only a 11% profit margin for the rest of the company ( $9 billion / $83 billion)
Do you seriously think Apple only makes 11% profit on iPad, Mac, App Store combined? No way on earth they make that little.
If we adjust the iPhone profit margin to 25% than the rest of the products make 17% profit margin. That is much more realistic.
Conclusion: iPhone profit margin is somewhere between 25%-30%. But highly unlikely that it is 30% or even 28-29%
It doesn't make much sense to calculate a per product profit margin. Business guys like to do that, but it only as little 'real' interpretation. The reason is that a lot of R&D expenses are shared between all iOS devices and there'll be lots of synergy effects with watchOS and OS X which can't be easily expressed in numbers.
Business guys tend to ignore that as they don't know anything about R&D.
Besides that... Are you really justifying apples attempts to maximize their profits?
In the end it's a commercial company, and of course they'll try to make as much money as possible. They don't give a flying f*ck if their business decisions are good for their customers, they'll just do what earns most money.
And charging +$100 for very little extra hardware expense is obviously a good deal for them. And as long as enough people are happy getting ripped of like that Apple will continue to do so.