Do airlines prefer pilots to use autopilot in cruise flight?

For the most part, yes. Workload management is a big deal in the cockpit. It cuts that work down. There are some instances where it's required to hand fly during cruise in the event of a mechanical failure. read more

Not only do airlines encourage using the Autopilot in Cruise flight, but it is actually a requirement at most normal cruise altitudes for a jet. Between flight level 290 and flight level 410 nearly worldwide we now have what is called Reduced Vertical Separation Minima (RVSM). read more

Airline pilots use it quite often. Simply put, the autopilot flies better then any pilot out there. It is also very fatiguing to manually fly the airplane for long periods of time, especially in challenging conditions (winds, low clouds,etc.). read more