Because it doesn't own the tracks, so it's at the mercy of freight company dispatchers.

But even if it did own the rails, population density and local transit connections and utilization are lower in California cities than in NEC cities. A trip from downtown Manhattan to downtown Philadelphia is not comparable to one from "downtown" San Jose to "downtown" Los Angeles; fewer people are starting or ending in either of the latter downtowns and they're probably going to drive.

The topography of the state also makes building high-speed lines on the most direct (coastal) route from San Francisco to Los Angeles cost-prohibitive, fiscally and politically/environmentally. The proposed new high speed lines all swing through the Central Valley, which adds even more time to the trip.