A large heart can be a sign of disease (heart failure, blockages or cardiomyopathy - rare and dont ask!!) but all these are easily diagnosed by even the most myopic doctor and are accompanied by symptoms such as breathlessness or pain or tiredness.
A large heart in young fit pilots is usually a sign of exercise. The more you exercise, the larger your heart grows as it is simply a muscle that needs to pump more blood. Many olympic sportmen have hearts twice as large as 'normal'.
Your young doctor should have asked you if you do lots of exercise, and you would have answered yes and thats that.
Unfortunately I cant be responsible for some of my colleagues.
good luck