Just like how your microwave maker doesn't support running different software on it. Apple is an appliance company hell bent on putting the user experience above all else. If this means 100% complete and total control over every instruction ran on the device, so be it.
That said, the motivation isn't malevolence, it's obsession.
A more apt microwave analogy would be if microwave manufacturer didn't want you to heat water in your microwave oven, because you could use that water to boil eggs outside the oven.
How many times do we have to make the argument that Apple doesn't run the app store to make a profit?
Please look at any Apple quarterly statement. There you'll see that the margins of the app store are in the low single digit percent range, whereas hardware has over 30% or even 40% margins.
That's what Apple is doing both with iTunes and the app store. Which doesn't mean this will always be the model - the rumored Apple TV could be different, there Apple could make most of its money selling services, while selling the hardware at cost. Maybe. Who knows. But the app store, and iTunes are merely feeder operations supporting hardware sales.
That said, the motivation isn't malevolence, it's obsession.