Automatic backups for MySQL Workbench
MySQL Workbench is a client querying and modelling tool and a very good one at that - it's purpose is not to perform server tasks - that's the job of the server. You can perform manual backups using Workbench, but I'm assuming that's not your long term goal.

There are many ways you can perform backups. Take a look here for 10 of them. Some of the solutions are OS dependent - basically, you have more choices if you're on Linux/*nix than on Windows (which are you?). Also, it depends on whether your tables are InnoDB or MyISAM (hope it's InnoDB!).

Two (other Open Source) backup solutions not mentioned in the post above are Percona's XtraBackup which can be cron'd or Zmanda's (which was mentioned in the High Performance MySQL book by Schwartz et al.). Another solution would be MyDumper - again a Percona backed tool (except this one also copes with MyISAM tables). 

If you're familiar with *nix and file systems, then maybe an LVM solution might be for you? Try here.

I would advise you to study the solutions available and do some testing and see which one best suits your requirements.