Trains are ideal for middle distances. About 1 or 2 hour flight equivalencies. DC to NYC, Tokyo to Osaka, SF to LA or Seattle, The Houston, San Antionio/Austin, Dallas triangle, etc. NYC to SF is not ideal for a high speed train, take an airplane then.
With a high speed train you can have downtown to downtown service, not need any security checks or slow onboarding / off-boarding processes and more, which eats about 1.5 hours minimum on each side.
I struggle to understand why you are so sure of this. Traveling by train is already far, far more popular than traveling by plane in most parts of the world, but you don't see security checks there.
Maybe if someone figures out how to slam a train into a skyscraper. This seems rather impractical though, as terrorist attacks go.
But that's what it took for air travel. Hijackings were even relatively common pre-9/11[1], and they didn't even bother to start locking the pilot cabin door (probably one of the only security measure implemented after 9/11 worth anything at all) until someone did something that extreme.
With a high speed train you can have downtown to downtown service, not need any security checks or slow onboarding / off-boarding processes and more, which eats about 1.5 hours minimum on each side.