It depends on the aircraft type being used. Old turboprops are almost always flown by hand in all flight regimes other than the cruise due to them having less sophisticated autopilots, assuming it's working in the first place that is! The same is true for some older jets. More modern aircraft will utilise automatics for a greater portion of the flight to reduce workload. Company SOPs also suggest how the automatics should be used but they will reflect the type being operated. There's no difference between cargo, charter, scheduled or Bizjets, it just depends on SOPs and aircraft type.
