Permissions give you more control over the players on your server. They allow you to prevent abuse from untrusted players. With permissions, you can give each player a specific rank based on their role in the server and how trustworthy they are. Let's say that you want to give a specific player the ability to teleport to the location of some other players. With permissions, you can do so without giving that same player the ability to spawn items, kick/ban other players, and even stop your server completely! The simplest example of a useful permission is not giving new players the permission to build. This prevents someone from logging on to your server with the sole intention of defacing the world. They will be unable to destroy your or other players' buildings.
When programming plugins, you can assign certain permissions to specific commands or actions. This allows you to give the benefits of your plugins to privileged people only. For example, you may want only...