"Eventually, TomTom agreed to pay royalties to Microsoft to license the three FAT patents."

That's not the case. Microsoft's own account of the settlement

http://www.microsoft.com/Presspass/press/2009/mar09/03-30MSTomTomPR.mspx

states

"The agreement includes patent coverage for Microsoft’s three file management systems patents provided in a manner that is fully compliant with TomTom’s obligations under the General Public License Version 2 (GPLv2)."

Paying royalties on copies of GNU/Linux would not be compliant with Tomtom's responsibilities (GPLv2 s7) as a distributor. Given Tomtom's commitment to rip out FAT from their products, it's possible that the deal was 'stop infringing on our FAT patents within two years and we'll give you coverage for free until then'. Alternatively it could have been a Novell-style 'we wont sue each other's customers once this deal is struck'. Either way - it cannot have been royalties on copies of GNU/Linux.