So Amtrak should suffer the loss of the revenue, "through no fault of its own"?
In the situation I described $1,000 represents my actual financial loss. Actual losses for common carriers would generally be limited to the cost of a phone clerk to modify my ticket and put me on the next train with an available seat. Which is probably somewhere around $15-$20. If no-shows were becoming a major problem a common carrier could add another $25-$50 in punitive fees to dissuade people from casually missing their trains while still honoring the spirit of the flat tire rule. In most cases under this scenario I'll still depart on the next train out and the carrier will lose zero money.
The solution, as Lonestar648 pointed out, is travel insurance.
Consumer level travel insurance policies generally cover things like being involved in the accident itself. They do not normally cover things like being delayed by an unrelated accident or break down.
I would modify my position somewhat, perhaps, if lets say Amtrak manages to sell the no show space at some point, and in such a case, return a portion to the original purchaser. Not sure how complicated that would entail....
Amtrak needs new passengers a lot more than new passengers need Amtrak. If Amtrak gets too heavy handed with their rules and penalties they risk suffering financial setbacks as Baby Boomers with pensions and disability checks and social security begin to die off en mass. Younger people on ever tighter post-Boomer budgets will end up looking for other options such as faster flights, easier car rentals, and cheaper staycations.