Yeah, I second this point. I don't know much about the situation between Microsoft and Android's OEMs, but to me, it seems like a simple case of "I've invested money in research, came up with some useful technology that you [the OEM, that is] are paying to use".

I don't see where the controverse is (other than the more general and complex debate about what should be free, etc..)

Consider that Apple own patents for pinch-to-zoom and the use of a gyroscope to control the rotation of a screen (turn the phone sideways, get landscape view). Given the thousands of patents all of the big companies own it becomes very believable that Microsoft would own a bunch of patents that many phones infringe on and that it would take Microsoft time to even realise it owned them (a possible reason for the delay in going after phone companies).

Patents that are essential to the phone being popular (can you imagine a smart-phone without the two above features).

Patents that would force most suppliers to just pay up.

EDIT: Just to confirm, I am agreeing with you, I just figured I'd explain why I think their claims are likely valid. This is not to say I agree with these patents being given but I've seen so many comments that seem to assume this is all a big con that will fall apart at the slightest scrutiny.