MS target right now is memory cards. Most flash cards are formated using FAT, just because it is easy and is fairly efficent when space is limited. MS has already said it will go after this market.
I would guess that MS will try to hit memory card makers with a sub-dollar per card fee. Going for the companies using the cards would be more sensible, but going after the card makers lets them blanket the entire market with a miniscule fee and still make a fortune. Trying to go after all the companies that make card readers and writers for different products would be much harder.
Jay