They admit that the current batch of high-speed rail lines being built, mainly California's, will run on new lines that won't interfere with freight. The Economist's worry seems to be about the more extensive proposed high-speed rail network that's currently on the drawing board, which is proposed to include extended portions on existing freight rails (at 110mph) to link together the purpose-built higher-speed segments. They seem to be thinking of plans like this one: http://www.fra.dot.gov/Pages/203.shtml
But is that really even a medium-term worry? I'll be surprised if even California's line gets finished by 2020. I would be very surprised if this more extensive national HSR plan that's supposed to follow later gets anywhere anytime soon. The map linked above is the result of a process begun in 1991, which has not been turning into a high-speed-rail network at any particularly great rate of speed. It'll be a miracle if they settle on a final plan by 2020, much less fund it or actually start building anything. I'll eat my hat if that entire network is built in my lifetime!