Military pilots are not unlike most other pilots: we're lazy and love booze, and we become just as autopilot crippled as the next guy.
Fighter aircraft controls are designed around the HOTAS philosophy, or hands on throttle and stick. To quickly perform flight critical functions, like disengaging the autopilot, the pilot's hands do not even have to move from the controls. On the Super Hornet the preferred method to disengage the autopilot is to paddle it off with the pinky finger on the stick. However, 5 pounds of pressure on the stick will also disengage the autopilot. Furthermore, some autopilot functions of the super hornet are always on. For instance, the jet constantly trims itself to 1 G and this autotrim will relatively help maintain a stable platform.
Aside from laziness, there are times when the autopilot can be a large asset to the mission. The cockpit of a fighter aircraft can get very busy when transitioning between phases of flight.
Here are a few mission related examples off the top of my head when having some form of autopilot is really nice:
- When leading another aircraft (it makes it easy for the wingman if you are stable)
- When flying parade and trying to do anything besides flying parade. Flying parade sucks.
- Configuring mission related instruments
- Performing coupled approaches to the boat (scary)
There are as many, if not more, reasons to use the autopilot in a fighter aircraft than in our civilian counterparts. However, as you rightly assume, when we are flying dynamically (ie, low levels, BFM, bombing, etc), the AP is disengaged (save autotrim), and the pilot controls the aircraft.