The benefits of permissions
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 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 would be to not give new players permission to build. This prevents someone from logging on to your server with the sole intention of defacing the "world". They would be unable to destroy yours or other players' buildings.
When programming plugins, you are able to 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 only want your good...