Is the preference for not taking payment for Ruqyah something known only to Allah, and can a Raqi who takes payment donate it or use it to develop his work in a way that benefits the general public?

The preference in performing ruqyah is by seeking reward for it, not by taking a wage. However, taking a wage might become preferable for some if it leads to good deeds, such as taking money to feed oneself and one's dependents, or to perform virtuous acts that cannot be done without money, like Hajj, Umrah, Jihad, and charity. Indeed, a person might be granted in a less preferred act what is not granted in a more preferred act.