I wouldn't go so far as to say that NTFS and FAT32 are similar. I won't dive into the technical details of why they are completely different. NTFS is much more robust than FAT32, and beyond filesystem-level security it also supports filesystem-level encryption and filesystem-level compression. It's much more efficient about disk usage than FAT32 (where cluster sizes get rather large as you approach large partition sizes).
The added robustness is reason in itself to choose NTFS if at all possible. When WON'T you use NTFS?
(1) If you need a partition to be visible to a Win9x installation on a multi-boot system
(2) If you really want to be able to get in with a boot floppy to fix things, you'll put the OS only on a small (1GB) FAT32 partition and format the rest as a working partition with NTFS. This is really not necessary with Windows 2000 because it offers a "safe mode boot" that Windows NT didn't have.