Boomer:
Here's my guess on why Amtrak is less expensive on the West Coast. Amtrak is divided into 3 semi-independent sections:
Northeast, West Coast and Intercity (everything else) with the ability to set its own fares for that region. In the Northeast Amtrak does compete with the Shuttles so it prices fares near but below
what the airshuttles charge. On the West Coast Amtrak doesn't compete very well with the Airlines (except possibly LA - SD) so sets fares to get the vacationer not the Businessperson. In other words, its not that West Coast fares are low but that Northeast fares are higher because of higher percentage of business travelers.
Or not!
Just my guess!