In the airline environment, various policies and regulations don't permit the pilot to hand fly all the time. In most RVSM airspace, for example. With advanced levels of approach and landing capability, many aircraft are landed on autopilot, as most pilots will agree that the airplane does a better job than they do...to a point.
That said, I've always preferred to hand fly where I can, regardless of what I fly. Some aircraft and some operations are always hand flown, of course. In other cases, I have to make myself use the automation in order to stay proficient with the automation. It can add another level of safety to the operation when used properly, and one should stay just as proficient at automated operations as hand-flown operations...otherwise one might handicap one's self.
I've met pilots who engaged the autopilot as soon after takeoff as possible, and who disengaged it at the last possible moment before touchdown, or in the case of category III landings, not even then...pilots who didn't want to hand fly at all. I actually saw a pilot panic and consider diverting and landing once because the autopilot failed and he had to hand fly. I've also seen more than a few pilots who became uncomfortable at the idea of having to navigate without a magenta line to follow.
I recently was involved in an operation that required the pilot to make a series of mental calculations while flying airborne patterns in the dark above a target, mostly on instruments. The head work could become taxing after a while, and with four or six or more hours of this, hand flown, the effort could become tedious. A display on board would draw a track on a moving map. If the pattern was flown correctly, after a while, the pattern would be depicted on the map. Then it became a matter of simply following the picture on the map.
What I learned after speaking with other pilots was that they usually did this very thing. I also learned that using the math formula was nearly unheard of among many of the pilots, even though that formula became very important when doing various types of required actions in flight. Essentially, they'd become complacent because they had a colorful picture to follow, rather than maintaining the elemental skills involved in that job. Ultimately, they were able to do their job very well, so one may say that their choice didn't impact performance...but I think it does give some insight into the effect of automation, displays, systems, and so forth, on an individual's tendencies in the cockpit. Like water and electricity, pilots tend to take the path of least resistance.
The problem arises when these inconveniences become inoperative or malfunction, leaving the pilot worse off than before, as now essential skills have eroded.