That's true. I cannot prove there is no God up there listening to prayers. The same way you cannot prove there isn't an invisible pink unicorn up there watching over us (
http://www.palmyra.demon.co.uk/humour/ipu.htm). It's hard to prove something doesn't exist.
The problem with God and prayer is that there is no proof that they do exist. In fact, there is no rational reason whatsoever to think that prayers might be heard - after all, people are praying all of the time, and there is no indication that any of them have ever been answered.
The one thing there IS proof of, however, is that the Bible - the foundation of Christianity and Judaism, is wrong. There are many things in the bible which have been proven to be untrue. Now, if this flawed book is the basis of somebody's religion, and it is based on this religion that a person says prayer exists, then I would say that they are on pretty shakey ground. This of course doesn't prove that prayer doesn't work, it just shows that for Christians and Jews at least, there is no reason to believe that prayer does work.