According to http://arstechnica.com/open-source/news/2009/04/linux-foundation-says-its-time-to-ditch-microsofts-fat.ars
Because Microsoft and TomTom have settled their dispute. Apparently TomTom used the Linux kernel for their GPS, which contains FAT support which is a no-no slap in the face for M$.
TomTom Counter sued M$ based on the fact that they stole some navigation like stuff. TomTom now has paid to license Microsoft’s patents, including those covering FAT, However they are going to weed it out and remove it in the next couple of years.
Although the settlement has ended the conflict between Microsoft and TomTom, questions still remain about the implications for FAT in the broader Linux ecosystem. Microsoft has previously stated that this lawsuit represents an isolated issue and that the company does not intend to broadly sue Linux users. Upstream kernel developers could potentially adopt TomTom’s code changes in order to avoid future patent disputes with Microsoft over FAT.
But being a paranoid people we (linux users) are they are going to try weeding such old and out dated filesystems out of the kernel in the not too distant future.