Lately, there have been several deals between Microsoft and several Linux distributions that involve cross patent indemnifications and technology cooperation agreements. These deals have caused much comment and concern within the Linux community. There is a miss-trust of Microsoft (rightly so in my opinion) and a fear that this is a plot on Microsoft's part to harm Linux.
I suspect that Microsoft is trying to protect its future; that Microsoft sees, as many commentators have noted, that Linux is slowly winning on the server and desktop fronts in governmental, military, and educational areas. Also Linux is gaining in Asia, the Pacific rim, Africa, South America, and even in Europe. I suspect that Mircrosoft prefers to get the total sale dollar in the sale of software, but if it can not get all of the sale, then it wants at least a part of the sale and that this is what is driving its recent deals with Linux providers.
I do not think that the paten indemnifications are past oriented, but rather are future oriented. Without such indemnifications, no distribution can include software that lets users (especially desktop users) use Microsoft products (or compatible software) such as meeting, messenger, outlook, etc. I think that Microsoft is laying the ground work to keep it from finding its products excluded in areas where Linux replaces Windows. I don't think that the Kernel is involved as much as kernel loadable modules and user area software. The real issue is that if the software uses Microsoft developed and patented software, then no Linux distribution can use it without Microsoft's permission.
As the reaction to the Novel deal has shown, there is likely to be a very adverse reaction from the Linux community when a distribution enters into an agreement with Microsoft, and thus a tendency for distributions to refrain from using Microsoft compatible software if Microsoft's permission is required. The patent indemnification provides the distribution with a competitive advantage (i.e. legal Microsoft compatibility) as well as the legal framework for including patent protected software. It also gives Microsoft a way to get distributions to share in revenue.
Microsoft has made it clear that they see a big future in the SMB area as well as the home entertainment area (i.e. digital convergence). Linux, with its cost advantages, resistance to viruses and intrusion, and stability, has an appeal to vendors servicing the SMB and home markets. While Microsoft can slow Linux's penetration into these markets, it can not stop it and it is almost inevitable that Linux will dominate or at least gain a large market share. Mircrosoft is trying to ensure that it will be able to participate in these markets, even if it loses its monopoly advantage.