#2, planes are dirty and we lack the technology to make them clean. Perhaps by the time HSR is built, we'll all have solar-powered e-fuels, or a major battery revolution that enables electric planes. But we don't have that yet and it's not clear we'll have it any time soon.
#3, the flying time between LA and SF is quick, but there is much time getting to airports, waiting at airports, delays at airports due to weather and inbound flights, and getting back to city centers.
#4, there are all sorts of other locations on the route. For instance, the Bay Area is a major economic center, but housing is extremely expensive. HSR enables people to live in Stockton or Modesto and get to San Jose, or Oakland in under an hour. It will invigorate Bakersfield, Modesto, Stockton, Fresno, Madera.