Find unused public and protected methods in PHPStorm

It's not possible with PhpStorm 6. Here is a snapshot of the Project Settings (where you can set those options):

The following only works for private methods.

It's possible in PHPStorm 7/8. Go to Code > Inspect Code and use a custom inspection profile. In the Inspections window, click on Add and unselect everything except PHP > Unused.

Inspection profile creation:

Inspection scope