You can't take that statement at face value. Part of the point of prayer is to focus your mind and block out irrelevant thoughts and stimuli. (Is it not?) I'd like to see how brain activity of people praying compares to those in meditation.
Except, that's not what the article is talking about. It was not the person praying that had their activity shut down, but the person hearing prayers. And not prayers in general, but only when coming from someone they perceived to be a "healer", but not prayers by an "ordinary" Christian.
Right.. I don't really like the wording of the statement. But the article makes sense though. If already believe in someone, your "doubt" mental processes shouldn't be firing.
teilo is right: this really has nothing to do with the act of praying, but rather people's brain reactions to those whom they intrinsically believe to be in a position of authority/power. Related to your question, I remember reading a few articles about this in the past. Essentially, brains deep in prayer == brains deep in meditation. (Quick search - this might be one of those articles: http://www.time.com/time/magazine/article/0,9171,995465-6,00...)
I'd like to see how the brain activity of people reading the article compares across religions. Do Skeptics become more or less skeptical when presented with a claim that seems to reflect negatively on religion? Are Christians more or less likely to be skeptical when reading the same claim?
What's the actual phenomenon being measured here? Is it a shutting down of skepticism due to prayer, or due to trust, or something else?