In order to keep Apo Island green and clean they are charging money from tourists and visitors to visit the island. These fees are displayed on a big sign in Malatapay so you can read it before you rent a banca boat to go to Apo Island.
These charges are collected on Apo Island in the registration office there when you arrive. There are different rates for tourists / local residents of Dauin. They figure local residents of Dauin pays their dues through taxes as well.