Excellent article. This sort of thing is why I subscribe to LWN.
And now, I'll do something I've probably never done before, try to write how things might look from Microsoft's perspective.
Microsoft licenses its FAT patents to probably pretty much all corporations that want FAT compatibility, which (sadly) is a quite a large group due to FAT being commonplace.
So, to Microsoft, TomTom is the odd company out, a strange corporation that won't license its FAT patents. It's possible the Microsoft lawyers couldn't care less what OS TomTom runs (or perhaps don't even understand much about OSes) - to them, TomTom is just another company, that 'should' license the patents just like everyone else. Or, perhaps the Microsoft lawyers are aware of Linux being in the picture here, but think, why should we give a free pass to TomTom just because they happen to run Linux?
So, I'm not terribly surprised Microsoft decided to sue. The problem is the US patent system, and corporations that support and utilize it, like Microsoft.
Overall, I think the lawsuit shows Microsoft is not willing to give Linux a pass, which is a bad sign - but not as bad as a direct and all-out attack. Or, if this is an all-out attack, and FAT patents are the worst Microsoft has to hold over our heads, then I'm pretty relieved, all things considered.