In the unzipped folder is a folder called mmd_tools. Copy the mmd_tools folder into Blender's scripts/add-ons folder. After opening Blender, click File, User Preferences. In User Preferences, Add-ons, ...
You need to open Blender AFTER installing a new add-on. Blender detects a new add-on when it is starting up. One of the most common errors that people make when ...