It was the Master who ridiculed the idea as 'prayer', just as many of you seem to be doing. Neither the Doctor nor Martha claimed any such thing. They merely stated the mental energies of the entire population of Earth were being channeled into the Doctor by way of the Archangel system. Apparently, the Doctor deduced the signal was a two-way street. It had never occurred to the Master that his system could be used against him.
There is one mystery, though. The Doctor reversed the effects of the Master's laser screwdriver with the energies he received from the Earth's population and restored himself to normal size and appearance. How did his tiny suit expand to fit him as a full sized humanoid being when it was tailored for a tiny, Gollumlike creature? After all, his usual suit did not shrink with him. This, in my opinion, was the major plot hole in the episode.