I'm inclined to agree with this theory. Ironically, much of this article is also FUD. i.e.
The deal could be seen as a veiled threat to other handset makers choosing Android - if they don't have such an agreement in place then presumably Microsoft is at liberty to sue them for patent infringement?
theregister fails to take into consideration that MS is a longstanding partner of HTC's and that HTC was making WM phones almost exclusively until the last year or two. It's very likely that this is the result of an agreement made long ago.
