When you deploy bigger planes you also need bigger infrastructure: The A380, for example, has had some delays due to new requirements. [0] And the A380 itself is not the largest plane ever built [1] - the sizes we've standardized on are an economic tradeoff of land availability, energy consumption, and carrying capacity.
Finally, it's not just planes that a train competes against, but automobiles; simply, if more people drive, we waste more energy. The state's planners have run the numbers and determined that HSR will diversify the transit capacity cost load and make it less risky to hit capacity targets 20 years out. [2]
In current urban planning practice, rails are preferred as a way to encourage dense and sustainable development; when you go downtown-to-downtown, the land value around those hub stops skyrockets. The Japanese rail system was built around this principle, encouraging the rail companies to be real estate investors as well as transportation companies - as a result, the trains go to nearly every major destination. In the case of CA HSR, the stops in the Central Valley will become secondary hubs for businesses that want equal transit times between SF and LA. This puts the Central Valley towns on a more stable economic footing and is good for the overall welfare of the state.
[0] http://www.airliners.net/aviation-forums/general_aviation/re...
[1] http://en.wikipedia.org/wiki/List_of_large_aircraft
[2] http://www.transformca.org/sites/default/files/moving_ahead_... (page 31)
