Apple marks up the price of the iPad over the hardware costs, some of this includes paying for the iOS engineers.
6 of one, half a dozen of the other.
It's just that Apple is more efficient at producing the entire thing than Microsoft+Intel+Samsung are.
Microsoft charges a license fee that they believe will maximize their total revenue (units sold multiplied by price). Fair value is only indirectly related, in the sense that a grossly high unfair price would reduce their total revenue.
Most of the complexity lies in the gui elements added by the manufacturers (TouchWiz, HTC Sense, etc) in an attempt to differentiate themselves from the rest and foster brand loyalty.
In any case, I don't think the software customization cost per unit in android phones it's anywhere near those MS license costs.
Only if you want to ship an SoC already supported by Linux. (Even then, there is tons of board specific code.) If not, you are looking at a very non trivial amount of work.
You have an extra layer of overhead with a Microsoft device vs. an iPad. Plus, because Samsung, HTC, etc are all making the devices, they cannot come close to the economies of scale that Apple does.
Apple's model is very clever. As a niche player until recently, they had to be more clever to survive. Look at their product lines -- they all share lots of components.
While I get what the author's saying here, it's a bit disingenuous to call either of those situations "free". Both companies invest nontrivial amounts of money into their OS. Apple develops their in-house OS, and Android is a "some assembly required" product.