Why are these directories called file systems?
The term "file system" has several meanings. When people talk about the file system names like ext4, UFS, NTFS etc. they have in mind the organization of data storage at low level (in terms of blocks on media). Such "file systems" usually requires driver to access data stored on media formatted with that file system. In the case of /proc, /usr, root file system or something file system simply refers to a directory structure.
Technically in Linux any directory can be a mount point for file system. This allows you to select the best type of file system (ext4, ufs, xfs etc.) for individual directories, depending on the nature of the stored information and security requirements.
I believe in your case those directories are called "file systems" because they are are often used as a mount point for individual file systems. /proc is always a mount point for the procfs pseudo-file system that presents information about processes and other system information in a hierarchical file-like structure.
There are a few directories which can be considered file systems: /dev, /sys and /tmp.
/proc is a very special folder, and it is not stored on disk, but in memory and is used to give info about system (CPU, RAM, devices..). So it use a special File System (not ext4) that is called procfs. You can read more on Wikipedia: procfs
Instead, /usr, /var and /home are generally (at least on a desktop computer) stored on the same file system (e.g. ext4), and often on the same disk: they are regular folders, with specific meanings. Always on Wikipedia you can find detailed info on Filesystem Hierarchy Standard.
They are not really "file systems", but this paragraph help explaning this naming usage (from FHS 2.3 reference):
To boot a system, enough must be present on the root partition to mount other filesystems. This includes utilities, configuration, boot loader information, and other essential start-up data. /usr, /opt, and /var are designed such that they may be located on other partitions or filesystems.