Ticket to Ride: May a train segment count for 2 different routes?
From the rule book:


  The object of the game is to score the highest number of total points. Points can be
  scored by:
  ◆ Claiming a Route between two adjacent cities on the map;
  ◆ Successfully completing a Continuous Path of routes between two cities listed on your Destination Ticket(s);
  ◆ Completing the Longest Continuous Path of routes


You shouldn't think of it as building trains, but as claiming routes. The plastic trains are only there to show that the route is yours.
Once you've claimed a set of routes between Atlanta and San Francisco, you can (and should) use and re-use this route as often as possible.