In the Season 6 episode "The God Complex", a hotel with constantly shifting rooms is the hunting ground for an alien creature which feeds on faith. Joe describes the process and we see it in action a few times. Once one encounters his or her most primal fear, it triggers his or her faith in defense. The person continues to run around until their faith is at it's highest, the alien catches up, the creature feeds on the faith of the person, and the person dies.
About 31:00 in, the creature is following Rita who has started wandering around the hotel. She's seen her worst fear much earlier (of disappointing her father) and has been kept strong by her Muslim faith. The Doctor is wandering the corridors looking for Rita when he finds "Room 11". He looks in, his pupil dilates in surprise, we hear the cloister bell, he makes the comment "Of course... Who else", before closing the door and sticking a do not disturb sign on it. The Doctor has started 'cooking'. In time he might also start to praise him. It may just be as simple as the fact that he has not had long enough to cook.
One other possibility might be based on what his most primal fear was. If one's biggest faith was also his biggest fear, it could create a very circular problem. More fear would inspire less faith. For example, if the Doctor's biggest fear was himself letting everyone down, the more self-confidence he had would mean the less faith he had to feed the alien with. His own lack of self-confidence may be what gves him the push to leave Amy and Rory behind at the end. But all of that is wild speculation since we don't know what's in the room (other than the sound of the cloister bell).