An operating system's file system structure is its most basic level of organization. Almost all of the ways an operating system interacts with its users, applications, and security model are dependent upon the way it stores its files on a storage device. It is crucial for a variety of reasons that users, as well as programs, be able to refer to a common guideline to know where to read and write files.
A file system can be seen in terms of two different logical categories of files:
Shareable vs. unshareable files
Variable vs. static files
Shareable files are those that can be accessed by various hosts; unshareable files are not available to any other hosts. Variable files can change at any time without any intervention; static files, such as read-only documentation and binaries, do not change without an action from the system administrator or an agent that the system administrator has placed in motion to accomplish that task.
The reason for looking at files in this way is to help you understand the type of permissions given to the directory that holds them. The way in which the operating system and its users need to use the files determines the directory where those files should be placed, whether the directory is mounted read-only or read-write, and the level of access allowed on each file. The top level of this organization is crucial, as the access to the underlying directories can be restricted or security problems may manifest themselves if the top level is left disorganized or without a widely-used structure.
However, simply having a structure does not mean very much unless it is a standard. Competing structures can actually cause more problems than they fix. Because of this, Red Hat has chosen the the most widely-used file system structure and extended it only slightly to accommodate special files used within Red Hat Linux.