I have been asked this question many times by many people.
What is better autofocus or manual focus? And the answer is really not simple and straightforward.
The mode of focus will depend on a lot of extraneous factors, top among them being light conditions and mode of shooting.
I will try to explain how these two conditions affect the focus we choose.
Most DSLR's nowadays boast of a excellent six and nine point auto focus and the results are quite good.
But there is a rider here.
Autofocus essentially works by trying to differentiate contrasts.
Like for eg if the back ground were to be dark, then the autofocus will focus on any bright object in the fore ground and vice versa.
But what if there is no bright object in the fore ground? The auto focus will not be able to work.
To overcome this problem, many cameras use a system wherein a small amount of light is used to illuminate to fore ground while focusing (You might have noticed this yourself, when shooting in poor light the light in front of the camera usually neat the lens lights up intermittently).
However this is not very effective and the autofocus may end up focusing on a point which is not of your interest.
In these circumstances, it is best to use a manual focus.
I personally prefer manual focus in conditions of poor light.
Autofocus also does not work well at extremes of zoom.
SO I prefer to use the manual focus instead.
Personally I prefer the manual modes everywhere but autofocus will work fine everywhere except the above exceptions.
So the choice of focus is completely yours with the riders mentioned above.
But there is one instance where I consider autofocus mandatory.
This is when I use the continuous shooting mode.
I use this mode for action photography like sports photography.
In continuous the camera is shooting at high speeds( Some cameras can shoot at 16 frames per second).
So it is nearly impossible to use the manual focus here.
So I always use auto focus in these situations.
But for all other conditions I personally prefer manual focus because I feel that it gives me more control over the photo.
But autofocus will work equally fine except the conditions mentioned above, so if you are comfortable with autofocus, go ahead with it, just keep the above guidelines in mind and your photos will turn out just fine.