Since the airport extreme with a usb drive is essentially a NAS the file system won't matter, but what does matter is the network protocol. It's been a while since I've had a windows machine or even booted to my windows partition on my macs so I don't remember but I think you have to install Apple's Bonjour on Windows to see it. I'm sure if you go to Apple.com, under support and review the manual it will indicate what steps you would have to do.
I would stay clear of FAT32 and Apple probably won't acquire the licenses to write to an NTFS drive and besides the HFS+ is a better file system. Anyways, I don't think you have a choice with the filesystem on the Airport Extreme.