Snarky me wants to say that it's because Apple has been failing to obtain proper licensing for some of their tech and making a lot of money off of it in the meanwhile. We see some of that is catching up to them. Most of this comment is tongue-in-cheek...
Eh, I don't think this is very much of it. Patent cold wars. Apple owns a ton of the patents on multitouch and basic mobile computing tech. Apple can sue them for multitouch if they sue for patents on cell tech. Both companies would spend years and probably just end up getting each other's patents invalidated.
It's more about margins. Android manufacturers lack the ability to separate themselves from each other except on software; it's too easy to switch. Android users don't have brand loyalty. They'll buy Motorola one year and Samsung the next if it makes sense. So all the Android vendors have to either make extremely unique devices, or race to the bottom on price, or both, to stand out, because if they're $50 more expensive than their rival their rival gets the sales.
US Patents are a crazy thing. So much generic tech is patented because patent because patents are granted too easily.
And Android software tends to be...both more and less profitable. Advertising is more profitable because you can collect targetting info easier on your customers (Apple restricts app makers more), but sales tend to be less profitable because iOS users are bigger consumers and spend more money in general. The average iOS user generates far more traffic and actually makes Google more money. And so, Apple makes a ton of money by charging Google billions (yes, with a B) to make Google the default search for Safari.
So Apple's actually making money from Google paying them, *and* selling higher margin phones than the hardware manufacturers for Android, *and* making more on the app store (at least per user). They basically get the best of everything combined (a portion of Google's revenue with zero work, more money than any hardware manufacturer, etc).
Microsoft, interestingly, probably makes more money off of Android (they get some licensing fees for patents in Android) than they do off of Windows phone.