There are different methods to back up files and directories. However, to back up an entire tree of files and directories, cloning a partition (file system) is one of the most effective method. When multiple partitions are used, it is easier to clone only certain partitions.
Even though several partitions may exist on a single hard disk when a system is small, it is possible that each partition will one day occupy its own hard disk. The use of partitioning makes it trivial to transition from multiple partition on a hard disk to one partition on each of multiple disks.
The reliability of a system can be improved by partitioning. By putting all end user files into one partition (separated from critical system files), a run-away user program can use up all the space of the end user partition without affecting critical system functions.
When a system is mounted, there are options to specify who owns the file system and whether it should be read-only. Both of these options can help protect the content of files in a partition.