The file system you choose (FAT/NTFS) is independent of whether or not the device is bootable.
When you format a storage device (Hard drive, Floppy, CD/DVD, SSD or USB Drive) you have the option to make it a bootable device. If you choose to make it so, some essential system files are copied to the media. This allows the computer to start up and run without the normal drive that contained your OS.
A common use of a bootable USB drive these days is to load a new OS (a fresh install of Windows for example) when you don't have the CD, but you had bought and downloaded the electronic copy.