it can do more than phpmyadmin, providing you have access to the server via workbench. becuase PHPMyAdmin runs on a server you can manage the database withn say an remote ISP's firewall, whereas they may refuse workbench from an dynamic IP address.
Workbench can do more than PHP, sucha as change mysql settings, start and stop servers. from an adminstrator perspective I'd want workbench for me, and phpmyadmin for users