This short version of the answer is:
- The pre-Ottoman Emirates that ruled Asia Minor encouraged missionary activity.
- Once Constantinople was conquered, the Millet system was put in place, granting confessional communities autonomy. So long as the Christians provided taxes and troops, the Ottoman Empire was not particularly interested in converting them.
- Albania and Bosnia were an exception, and Islamisation was pursued there to quash ongoing rebellions.
Several answers on related questions provide further detail.