If I had to guess, I would say that he saw himself in the room. Perhaps an angry version of himself, or perhaps a version of himself that is all alone, or perhaps a version of himself that just doesn't care. Hard to say. But he says, "Of couse. Who else?" It's also possible he saw himself responsible for Amy's death, which prompted him to leave them behind.

It's interesting to note that seeing whatever it was didn't seem to activate the Doctor's faith mechanism, because he never started praising the minotaur.