"If people pray for rain and it rains, how is that? I would say: Nothing in particular. Just as when people do not pray for rain, it also rains. When people try to save the sun or moon from being swallowed up [in eclipse], or when they pray for rain in a drought, or when they decide an important affair only after divination - this is not because they think in this way they will get what they seek, but only to add a touch of ritual to it. Hence the gentleman takes it as a matter of ritual, whereas the common man thinks it is supernatural. He who takes it as a matter of ritual will suffer no harm; he who thinks it is supernatural will suffer harm...."
from the Confucian philosopher Hsün Tzu.
Vjack at Atheist Revolution has a post up titled Japan Doesn't Need Your Prayers, wherein he writes "If you are praying for the Japanese people, please recognize that you are doing this only to comfort or distract yourself. It is for you, not for them. It does not do them any good."
I agree with Vjack that if a person prays to God to help the people of Japan with the expectation that God's divine power will prevent any of the nuclear reactors from having a meltdown or causing trapped survivors to be magically kept alive until they can be rescued, then that person is deluded and is not helping in any way. A post I wrote earlier this evening, May God Protect Those Who Haven't Already Been Hurt Or Killed, was inspired by a comment I saw from someone on a Facebook post who falls into this category.
That being said, I don't think prayer and doing meaningful things to help are mutually exclusive. I'm sure there are plenty of believers in a personal god, whether Christian, Jew or Muslim, who will engage in prayer and then write out a check to a disaster relief organization or, if they are able to, volunteer in some meaningful way such as picking up or delivering supplies to be sent to the disaster zone to aid the relief effort.
For a religious believer, the act of prayer can serve as a ritual that can help to focus the believer's mind on a matter of personal concern, such as helping those who have been affected by a terrible calamity, and empower that person to take action. If the act of prayer really does have such an effect on a religious believer, then I certainly won't begrudge the believer's decision to do so, even if I don't personally think it is necessary.