With non-SLR AF systems there is no way to know precisely on what the camera is focusing. With AF SLRs the situation is better, although most have focusing screens with so little etching that this is sometimes a little of a guessing game as well. Even if you place a focusing frame on, say an eye, does the focusing element correspond exactly to the mark on the screen? With auto focus there is always an element of guesswork invovled. (The same could be said, however, about paralax error in a rangefinder as well.)
The biggest problem with AF cameras is that, depending on what AF mode you have chosen, the cameras will often not fire exactly when you press the shutter release, thus missing that all-important critical moment.
All this being said, I have an AF P&S and an AF SLR. Each has its own purpose and I use them according to their intended uses.
Kevin