As usual the Japan Times got it wrong. The ranking is not how friendly the nation is towards tourists, but how 'friendly' the economy is to the tourism industry. It's not directly about the experience that tourists have when they are here, but whether or not tourism industry can thrive and grow.
The categories used to rank the countries reflect this:
Sub-category 1: Enabling Environment
Sub-category 2: T&T Policy and Enabling Conditions
Sub-category 3: Infrastructure
Sub-category 4: Natural and Cultural Resources
When you look at these categories it's easy to see why Japan does well on this index.