Auto-flight is not necessarily an "on" or "manual" issue. There are different levels of automation that are appropriate for different situations and phases of flight.
The Auto-flight philosophy of the airline I used to fly for was as such:
Level 1: All automation is off; no flight director, auto-thrust, or autopilot. With the exception of visual approaches and deliberate decisions to maintain flying proficiency, Level 1 is essentially a non-routine mode. The use of Level 1 is solely to maintain flying proficiency or due to abnormal aircraft system operations. Level 1 is appropriate for any situation in which immediate and direct control of the aircraft flight path is required, for example, TCAS Resolution Advisory, aircraft upset, GPWS and TAWS warnings, windshear, and any suspicious, confusing, or unexpected response from the automation.
Level 2: Autopilot off, but at least one or all of the following in use; auto-thrust, flight director, or
FMC. This level is the primary mode used for takeoff, initial departure, and landings, except auto-landings. This level may also be used to maintain flying proficiency.
Level 3: Autopilot on and use of auto-thrust and/or flight director optional. This level is most effective when short range planning is needed (i.e. radar vectors, short range speed or climb/descent control). This level is used predominantly in the terminal environment when responding to clearance changes and restrictions.
Level 4: Autopilot on, auto-thrust, flight director, and FMC in use. Auto-flight coupled to the FMS is the primary mode for non-terminal operations and should be established as soon as "resume own navigation" or similar clearance is received. This level exploits pre-programming (such as LNAV departure) of the FMS. However, when significant modifications to the route are issued by ATC, it may be necessary to revert temporarily to lower levels of automation. Use of this level of automation during terminal operations must be limited to situations permitting advance preparation. Level 4 is not appropriate when last minute changes are issued by ATC or whenever time constraints prevent the crew from properly completing the advance planning necessary to safely operate at this level.
Retired 747-400 Captain