"A good directive is not application specific" is a very generalist statement. You should encapsulate DOM manipulation in a directive, so even if it's not as reusable as ng-repeat, if you have to manipulate the DOM it's the way to go as well.
The point is - "All DOM manipulation belongs to a directive" but still it can be made application agnostic. What he is mentioning there is making it application agnostic - like for example not assuming in the directive that you have $scope.users on the $scope etc..