Hey, Griff!!
Simply praying and expecting it to alter your physical reality, and then giving up when it doesn't happen promptly, is ignoring how the conscious mind affects reality, followed by an expected defeatist reaction that pretty much guarantee the effect will never occur. It takes a lot of practice along with skilled visualization, focused emotion, and strong belief in your ability to do so over a sustained period--depending on how great your level of practice is and how great your willpower and capacity to focus your emotion into the goal happens to be--to effect such changes. The greater the type of change you want, the longer it may take to manifest, again depending on the above factors.
Atheists obviously lack this belief underneath any prayers they may make in a moment of desperation, and thus do not learn to focus or visualize properly in most cases. As such, they can expect no results.
Quantum physics has clearly shown that human observations and thoughts have subtle effects on the reality around us, and the effect that the collective human race has on what we perceive as reality is likely to be profound. When individuals attempt to make such changes against the "consensus will," it obviously takes a heavy degree of practice, will, and focus (as noted above), which is why it can be so difficult, depending on the degree of willpower, experience, and focus when doing so. I have been practicing these techniques for about two decades now, asking for big things, and voila, two of them have finally manifested recently. I never expected it to be easy, but it's a natural scientific process that has nothing to do with faith and everything to do with the quantum nature of the reality we live in, and how the consciousness of sentient beings affect it on a largely subconscious level. The art described in human cultures as "magick" or "prayers" (its Christianized version) is simply a difficult to learn and demanding technique of affecting subtle and occasionally dramatic changes in your personal sphere of reality on a conscious level. Again, discoveries in quantum physics and the study of how human consciousness affects the sub-atomic realm over the past century make it clear that this process, regardless of what those considered "mystics" may call it, has a substantial basis in scientific reality.
The collective "consensus" will and belief systems of all sentient beings throughout the universe (assuming sentient life exists on any planet outside of our own, and it's logical to conjecture that it does) may be the basis of the "higher power" that religions have hi-jacked and conceptualized as "God," "Allah," "Jehovah," etc. This cultural interpretation affects how various human beings perceive this conscious aspect of the universe, but these mis-interpretations based on human preoccupation with politics and moralism does not render it scientifically invalid or "irrational." It's only human attempts to perceive it from a religious viewpoint, and the silly moralizing and political precepts placed on it (again, by self-serving human leaders), that result in irrationality.