With the train, you have way more freedom in choosing the time and the hour. You have multiple trains leaving during the day, and you can choose 30 min before needing to hop onto one. Also, if you miss one, you just wait for the next one.
Also, on the train you can work, relax and stretch your legs or eat freely. So it doesn't feel like lost time really. Planes often do, even if you travel business.
Meanwhile the Amtrak station in Seattle is centrally located, about fifteen minutes to downtown by tram. The Amtrak station in Portland is pretty much right in the middle of downtown. I don't know that I'd want to go from the Bay Area to Seattle on a train, but something like Portland to Seattle would benefit greatly from HSR (currently it's about a 4 hour trip).
I actually think that if the High Speed line is built all the way south to Eugene it kind of makes sense to build a traditional electrified rail way between Eugene and Redding CA. through Medford, and a higher speed line to Sacramento where it could interline with California High-Speed Rail to LA. Connecting Medford with Redding and Eugene with a traditional rail should be worth it on its own, but with the surrounding high speed lines it becomes possible to operate a west coast sleeper between Seattle and LA in like 10-13 hours (as opposed to the current 36 hours).
But more importantly though, this portion is very mountainous, making finding a high speed alignment without unrealistic amount of tunneling impossible. A traditional electrified train with speeds up to 120 MPH is far more likely to actually happen, and would do plenty to enrich the area as well as provide an alternative to flying between the Pacific North West and California.
The same light rail will take you anywhere from the airport in the south to the northern edge of the city. Within a decade it will go as far south as Tacoma. In a couple years a new connecting line will reach Bellevue. Eventually as far as Redmond (Microsoft). My own neighborhood of West Seattle will connect in 2035.
The future is bright for the west coast. If HSR connects us all this will be the most desirable place on Earth.