My only reason would be to hopefully transfer that password program to another thumb drive but I've got to find a program that will format the first partition as a CDFS drive. Windows will only see the first partition on a flash drive while linux will see all of them. Here's some other reasons to partition a flash drive:

http://www.rmprepusb.com/tutorials/multipartufd

http://gparted.org/why-partition.php

btw, GParted is one of the best partiton editors out there and it's free. I've used it several times when i was dual booting XP and Ubuntu. Just download it and burn it to a disk.