Careful here! There are as many Application Support folders as there are users, plus one for root. So if you have five user accounts you will find six Application Support folders. This is as it should be. The support folder at the root level of your hard drive provides the support files for any application for any user. If the program is installed in the Applications folder and the Application Support folder is in the Library at the root level, then the program and its support files would be universally available to any user when they log in.
Conversely, if the Support folder is only in your personal User account, those support files would only be available to you, no other user would have access to them when they logged in.