auto focus is generally far quicker than manual focusing can be - for sports, kids, pets and wildlife - action photography - auto focus is almost always used since it can lock onto the subject quicker than you can.
Further more the modern DSLRs do not have manual focus aids in the viewfinders as the older SLRs did - that makes manual focusing very tricky, especilly if the light is not perfect. Manual foucs does have advatanges, you know what you want in a shot to get sharp, the camera does not and if your shooting into (for example) bushes or through wire at a zoo there is a good chance that the camera will pickup on the closest thing to it - which might very well not be what you want in focus.
As a point I (and many others) find it easiest to set the af so that only hte middle af point is used - that way you can define the subject easily. It does mean that shots can come out looking very centred a lot of the time - creative cropping can get round this limitation