3 hours is about Osaka to Tokyo, a route that sees a massive volume of business travel on the bullet train in Japan, arguably far more than flying. SF to Seattle would be about 1300 km which is more like Hiroshima to Morioka, around 6.5 hours by train including a connection; I think at that point there'd be a split in favour of flying, but around a third of travellers would probably still opt for the train due to its comfort and convenience.
There's huge differences between the US and Japan. When I travel from my home in Tokyo to Osaka or any other city by shinkansen, I take public transit (Tokyo Metro specifically) to get from my home to Tokyo station or Shinagawa, and then transfer to the shinkansen. At the destination city, I just get off and either walk to wherever I'm going, or transfer to another local rail or subway line.
You just can't do that in the US, outside some very select situations (like going from somewhere inside DC to Manhattan NYC). From SF to Seattle, how do you get to the station in SF? In Seattle, how do you get from the station to your destination? What do you do to get around in Seattle? Generally, you need a car, which means renting a car, which is really expensive. The US is set up to handle this at airports pretty well: you get off your plane and go to the Hertz counter and pick up a car (and then after your trip is over and you've returned the car, get arrested for auto theft when Hertz reports your car as stolen--don't use Hertz). I haven't tried trains on the west coast, but on the east coast, I've never seen train stations set up with rental car counters.
