Cardiac hypertrophy is not necessarily a bad thing, it can be the result of positive adaptation, such as exercising.

Eccentric hypertrophy (athlete's heart) is the positive adaptation resulting from training the heart. The heart has a lower resting rate and is more efficient at pumping blood. It returns to normal size if training stops.

You'll never reach a state of hypertrophic cardiomyopathy (the bad kind of hypertrophy) with exercise. Its cause is usually genetic.