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, ...

One of the most common errors that people make when installing a Blender add-on is failing to restart Blender. Also you cannot install mmd_tools directly from the .zip file.