I guess it depends on how you define athletic. Being able to hit, throw and field a baseball aren't reserved to the athletically gifted. Running may be the only tool that all would agree is an athletic trait.
The
five tools are hitting for average, hitting for power, baserunning / speed, throwing, and fielding. Athletic would be more general, I would think. Physical strength and agility would be athletic skills that were not necessarily tools but useful in evaluating a player or a prospect. Some baseball skills like strike zone judgment and ability to read a ball off a bat might not be either tools or athletic skills.
I guess when people refer to Werth's athleticism they are referring to his speed, physical strength, conditioning, and the naturalness of his movement, while when they say he is a 5 tool player, they are referring to his hitting for average and power, run bases, strong arm, and ability to get to balls hit in his area.