It's worth pointing out that VirtualPC is not a PPC only application, and should therefore not be seen in that light alone.
Do Microsoft see it as a threat? Why would they do that, when more copies of VirtualPC in use most likely lead to more copies of Windows operating systems in use, each one needing its own license?
As to Microsoft's reason for this purchase, only time will tell. They might want to limit it to running Microsoft operating systems only, or they might want to be able to run Linux on XP servers (though I'm not sure why they would want to encourage that).
Is this a move against the PPC or Apple? I doubt that very much, though I expect to see development of the PPC version take a back seat in the future.