Menu Link permissions can be inherited from a "parent" folder or individual menu link permissions can be set on any menu link from the Website tab.
To view the permissions set on a menu link, right-click on a menu link, then click "Edit". Now click on the Permissions tab next to the menu link Properties tab.
Menu Link Permission Inheritance from System Host
Below is an image of a menu link that is inheriting all its permissions from the "System Host". This means that permissions on this menu link is inheriting permissions directly from the Role permissons themselves set at the System Host* level.
While editing a menu link, clicking on the Permissions tab and the "Permission Individually" button will stop any role inheritance coming from higher up the permission hierarchy and allows for permissions to be set on the menu link itself.
*For more information on setting permissions on dotCMS objects from the System Host, please see the documentation on Role Permissions.