On a digital camera getting things in focus is the hardest part for me and i worry manual focus is just pushing my luck.
As said, autofocus cameras give problems when focusing manually: the focusing screen is optimized for light transmission and not for focusing, the lens doesn't have a comfortable focus ring, it is likely too soft, too narrow, in the wrong position.
Digital cameras which only have an electronic viewfinder are the hardest to focus manually, and maybe this is the kind of digital cameras you are referring to.
Autofocus is superior for wildlife, sport, fashion, your dog (or your neighbour's).
In all other circumstance a proper manual focus is probably just more comfortable: you don't have to wonder which AF point is active, or don't have to focus/lock/recompose if your subject is not where the camera places the focus (typically the centre of the frame, or the nearest focus point).
A manual focus lens is probably more robust.
Also, an autofocus lens probably has "internal focusing" (IF). Focusing is reached by moving one lens element inside the barrel. In manual focus lenses it's either the entire lens (all groups) which is moved, or the front lens. This in general gives better optical performances than IF as far as I know.
Be careful about compatibility when you buy a Canon or Minolta lens or camera:
Minolta SR mount (also improperly called MD): Manual focus;
Minolta AF mount: Autofocus, and not compatible with the above.
Canon FD mount: Manual focus;
Canon EF mount: Autofocus (not compatible with the above).
Pentax and Nikon managed to use the same existing mount both for manual focus and for autofocus cameras, but there are incompatibilities you should be aware of when coupling something AF with something non AF.
Olympus OM, Yaschica/Contax (YC) and other mounts are mostly manual focus.
Fabrizio