When a person becomes passionate for a specific sport, seeing someone make a joke out of the sport can touch some nerves. If the athletes aren't going to take their "conditioning" seriously, is there really any reason for them to detract from another sport's workout or practice? A prime example is that some of the girls on the soccer team are sent to track and field to stay conditioned. But very few of these athletes do anything other than the bare minimum (and they even do that with little effort). This isn't entirely their fault though. Running is not a sport you can just throw someone into. In order to endure the self-induced pain of a long distance run or the intensity of a sprint, you must be serious about track. So as a result, soccer players are walking through their "workout" and taking up the time of the track coaches, time that could be spent coaching the actual track team.
Maybe instead of forcing the athletes into a program they don't care about, they could give the athletes a program of their own. If the athletes really want to improve in their sport they will follow that program. This way they'll be doing something that they will probably enjoy more, and feel is actually helping their sport.
Working out for any sport requires a passion or a drive for that sport. If you really want to improve you will do whatever your coach or trainer tells you, regardless of what it is.