NTFS is R/W under Windows (but not 95 or 98). Plus there are different "revisions" (or versions) of NTFS, so some NTFS features used by Windows Vista (or 7) will not be usable under Windows XP or 2000 or NT, etc.

Plus, Linux generally only supports reading from NTFS, but not writing. Yes, there are drivers allowing writing, but it's not 100% reliable (I guess they emulate Windows just a bit too much .

Plus, you want a USB stick (and MyDocs is just that) to work with all sorts of exotic devices, such as a TV, or an Android phone, or whatever, which probably only supports FAT32.

Plus, MyDocs/USB-stick are supposed to be used for exchanging data. Meaning you don't want any sort of file/directory permissions to ruin that "experience". This is, IMHO, the single most reasonable reason why VFAT/FAT32 is still so widespread.