Prayer is a powerful tool for improving the communication between the parts of your mind. It does not diminish its value just because the reassuring, super-intelligent voice in your head isn’t coming from the omnipotent creator of the Universe.
I’ve had a few experiences with meditation, and prayer is much like that. The focus and the feeling of ultimate goodness and nurturing are the same. I suspect that the emotional state of surrender to a positive, caring influence, and loving acceptance of one’s self as a valuable part of the Universe acts as a key to the improved integration of the mind. The result is a more full experience of the world and a deep respect for both who and what we don’t know first-hand. The latter result benefits both the individual and society: We individually experience less anxiety (fear), and society has fewer people trying to tear it apart for selfish gain based on a perception of other people as things to be manipulated.
I came to understand religion as the cultural manifestation of these realities, a way to explain them from an experiential (and not necessarily factual) point of view. It can teach practices that help people deal with their fears, increase their power, and strengthen their commitment to the welfare of their communities. Unfortunately, religion can also be (and has been) abused by those who perpetuate a simple lie: that the power of self-integration emanates from an external force that happens to be channeled through the manipulators. While the lie may be useful to initiate the process (like various myths aimed at children to keep them from hurting themselves until they become more aware), it must be shelved as soon as possible.
To argue against the lie in a public forum could threaten not only the power of the people who knowingly perpetuate it, but the success of the educational process it was designed to initiate. This is why, I believe, atheists like me are seen in a negative light by many people. While I have no problem with the former, the latter does bother me. We must find a better way to initiate people than to mislead them.