It seems like the prices only apply to rail travel between the listed cities. Here is something I copied from the Amtrak site about their rail sale policies:
Rail SALE purchases are non-refundable and may not be exchanged. Tickets may only be upgraded on board the train once travel has begun, subject to availability. Fares are subject to change without notice. Other restrictions may apply. Click here for more information.
Rail SALE fares may not be combined with any other discounts, fares or other promotions. Rail SALE offers are not valid in conjunction with Amtrak Vacations packages.
Rail SALE offers are valid for specific percentages off the full one-way fare on specific itineraries, based upon selections made from the Rail SALE menu at http://tickets.amtrak.com/Amtrak/railsale. Quoted fares are applicable only on specific service, itinerary, train number, direction, date, and time shown, for one-way travel between most cities listed, or most Amtrak rail stops in between.
Rail SALE fares are valid for reserved coach seating only and are not valid for the Canadian portion of joint Amtrak/VIA Rail Service. Rail SALE offers are subject to the restrictions outlined in the Rail SALE menu as they apply to the specific date and itinerary described in the menu.
Unless specifically listed as a Rail SALE fare, the return portion of a roundtrip itinerary may not be discounted. Rail SALE discounted fares vary according to specific offer.
Rail SALE fares must be purchased online via credit card only at http://tickets.amtrak.com/Amtrak/railsale. Rail SALE fares are not available for sale at Amtrak ticket locations, reservations counters, on board trains, or through travel agents. Once purchased, tickets may be received through ticket-by-mail, Express delivery, staffed Amtrak station or a Quik-Trak machine.
Rail SALE discounts apply to most points on the route between the origin (From) and destination (To) shown: your travel segment may begin and end at the origin and destination listed or most Amtrak stations in between. Enter your exact origin and destination to find the applicable Rail SALE fare.
Amtrak reservations agents and ticket clerks may not book Rail SALE offers. Purchase offer is made directly and exclusively via the Internet at http://tickets.amtrak.com/Amtrak/railsale.
Discounted prices may be rounded up within one dollar.