I wouldn't find it inconceivable for prayer to have some role outside of the belief in supernatural communication with spiritual beings. In a certain sense it's a form of meditation. If you change the wording of a prayer away from the implication that someone out there will hear you and make supernatural changes in the world accordingly, you could pray as a sort of meditation on a desire or on a value. I guess, at least, that repeating to yourself that you hold a certain desire and care deeply about it is a way to reinforce it.