The article states that Tokyo was among the list of most-often visited and familiar international cities. So, no Tokyo wasn't rated any higher than, say, Utsunomiya. Its just that Utsunomiya wasn't in the list to begin with (tourist-worthy thought it may be*). Also, I just reread Thomas's original post, which might give some hint as to why Tokyo ranked slightly lower than other cities.
Driving under the influence. According to the State Department, "The blood-alcohol limit in Japan is 0.03%. Punishments can be up to $10,000 in fines and up to five years in prison."
However, it feels like a very spurious reason to give Tokyo low points, as tourists to Japan aren't likely to be driving anyway. Kind of weird. What first sprang to my mind was harsh scoring from women due to harassment/molestation on public transport, but as Thomas's post states, women rated Tokyo highest for safety. Which means the low marks must have come mostly from men. The Roppongi drink scam hypothesis might be true - but that also feels very strange to me because its a specialized (and fairly localized) kind of threat, very easily avoided and most tourists probably aren't in a position to be affected by this. But who knows...the repeated warnings from the embassy must mean a lot of American dudes are falling prey to this scam.
* Just kidding. Utsunomiya can be safely left off of your tourism plans. Utsunomiya-stans, don't @ me.