You need to create first that directory. For example, you want a controller app/controller/admin/AdminController.php, first create the admin folder on app/controller, then you can do php artisan generate:controller admin/adminController.php. I am not sure if this coulde be done using Resouce.
Also routing in laravel is different with routing in CI. CI depends on domain.com/controllerClass/method/args and laravel is different.