Do your flight costs include parking, the costs of getting to and from the airports, the value of your time, the mental hassle of airport security theatre, the costs of additional luggage and so on?
"Fair" depends on what you're using it for. Parking at airports can be expensive, but parking at Tokyo or Kyoto station is more so. The stations themselves are more confusing and less well-signposted than an airport. And if you want to take oversize luggage (e.g. a surfboard) that's a moderately priced upgrade on a plane but completely impossible on the Tokaido Shinkansen.
No comparison is perfect. The best you can do is talk about both the positive and the negative so that people can understand and make the best choice for their circumstances. Price should absolutely be a part of that conversation.
