This is a matter of personal preference. I prefer not using the root account except when absolutely necessary. Writing to an NTFS partition from Linux using the root account involves a certain amount of risk. I wouldn't want to accidentally corrupt my bootable Windows operating system. Or worse, be responsible for a reader accidentally doing this to their previously working laptop!
While FAT32 is not secure or particularly robust, I think its "vanilla" nature makes it adequate for storing non-critical data that you want to share between XP and Linux. You'll just want to make sure you have a back up copy of anything you really can't afford to lose.