Dan,
Taking "extreme rookie" at face value and hoping to educate some more
Are you using the single (selectable) focus point mode for AF?
Are you using either AF-S (static), so it beeps when focused?
(the aim above is for you to be in control, not have the camera 'second guessing' and giving you unpredictable results)
Are you putting the single focus point onto an edge, not a surface?
Let me elaborate on that last question with a little explanation.
AF doesn't work well on surfaces (or low contrast edges); e.g. the cheek of a face, or the nose against the cheek, or the surface of a leaf
AF works better on detecting high contrast edges; i.e. a boundary between light and dark picture areas; e.g. the eyes of a face, or the edges of a twig/branch/leaf, etc.
It matters which direction an edge is in relation to the AF point.
The centre AF point works on both horizontal or vertical edges (it is sometimes known as a 'cross type' AF point)
You will notice the other AF points are rectangular and ideally the edge needs to cross the long edge of the AF point
So if you follow the above advice; set single AF point and AF-S modes and use the other information to choose what you focus on, it really should be better than manual focusing - assuming you're not trying all this in very low light, or with the polariser on, either of which will cause more problems.
Cheers,