No matter who you are, Spotlight will try to search all of the folders on the machines. However, it searches as you, and so it can only see files which you could see yourself. If you're root this means everything, but for most ordinary users it can't get into folders belonging to other users unless they've explicitly reset the permissions on those folders to allow it.
If you'd like an extra level of assurance, use FileVault. FileVault stores Home "folders" as encrypted disk images, so your files do not actually exist as separate entities on disk. Spotlight will try to index the disk image, but because the image is encrypted Spotlight will see only junk. Meanwhile, when you log in, Spotlight will index your drive as though it were a separate hard disk, but because of the way permissions work only you will be able to access it.