What I meant is that it could be much, much better. The article you point out hints at some of the issues: The inter-mingling of passenger and cargo trains ends-up seriously affecting the potential performance of cargo trains.
With regards to it being an absurd idea. Well, of course it is! And so is the case for nearly every idea that sparked a revolution in technology and thinking. The earth NOT at the center of the universe? Absurd! The earth not flat? Absurd? Everyone needs a computer on their desk? Absurd!
Not that I am comparing this to any of those shifts in technology. What I am trying to point out is that being open minded enough to even consider the seemingly absurd is an important part of discovering new ideas and developing new technologies. I always consider the absurd. I have hundreds of ideas catalog that are probably absurd. The alternative is to discount everything as ridiculous without even giving it an honest look. I just don't do that.
For example: Could this high speed train take the form of an underground tunnel connecting both coasts? This is absolutely ridiculous and probably even insane to consider. However, I take the approach of at least doing the research to try to get a sense of proportion in terms of cost and technical feasibility. For example, would there be an important mining element to the project that could offset the costs? I don't know and I am not trying to argue for a 3,000 mile tunnel. All I am saying is that I believe that it is very important to give seemingly ridiculous ideas a chance to be explored and, if need be, discarded based on data and not knee-jerk reaction.
The US freight rail system is the best in the world.[1] We move 10x more than Europe most years on a tons times distance basis. The running gear may look antiquated, but the fundamental numbers are staggering.
"No, the idea is that a new highly-efficient, all-electric, highly-automated and cargo-only transportation system be built with the express purpose of moving container-based cargo from coast to coast (and port to port) at the highest possible speed and lowest possible power consumption."
There is very little demand for raising the speed of freight rail in the US. Speed generally compounds inefficiencies.
Freight handling is by and large already automated and container based in the US rail network.
Existing electric designs preclude the use of double stacked container flat cars, one of the keys of US freight efficiency. Perhaps you have an innovation here?
Building an entirely new high speed electric rail network for freight is an absurd idea. I don't think you've even begun to model the economic realities, particularly the capex of building a new rail network radius'd and graded for high speed, with all above grade crossings.
[1]: http://www.economist.com/node/16636101