OK. I am a longtime lurker, but I suppose that this issue has roused me to post.
I suspect Amtrak doesn't really mind the status maps that much (they've gotten much better in their on time performance after all) but HATES Amsnag. Why? It goes back to how carriers price their services.
Yield management was invented by the airlines. Economists would call it "price discrimination", which sounds nefarious but really isn't. With every product or service, there are people who are willing to pay more and people who will only buy it for less. If you charge one fixed price, you lose potential revenue from both groups.
So pricing strategies are all about trying to make it possible to charge different groups different prices. This is why supermarkets have so many club cards and coupons- the price sensitive bargain hunters can claim discounts while those who don't care will often pay full price.
The problem is, transparent pricing tends to turn everyone into a bargain hunter. The old saying in the airline industry was that the business traveler in 10A who paid $1000 could never find out that the leisure traveler next to him paid $200. Of course, that oversimplified things a bit, but the basic principle was true-- the more transparent your pricing is, the harder it is to discriminate. In industries such as Hollywood where nobody is told what anyone else is charging, price discrimination is rampant.
We've already seen airlines being forced to cut costs because the Internet made their pricing more transparent than it was when you had to call or bug a travel agent.
Amsnag took that one step further. Since multiple searches are a pain, Amtrak surely feels that some people give up and end up paying a higher fare than if they had all the data in front of them. That's why Amtrak's own site doesn't provide the Amsnag capability.
Amsnag is a threat to their business model. So they moved to shut it down.