Loss of confidence sets in and soon the pilot convinces himself that twiddling the automatics and pressing buttons is easier than hand flying.
It also contribute to delay the acceptance and reaction to some new situations since you also have to decide "abandoning" the automatism before taking over.
In the Turkish accident the FO's reaction to the stick shaker was only to increase thrust, without simultaneously disconnecting the AP...
That's also a point I was trying to make in the BA038 thread where the PF didn't take manual control as the automatism was maintaining an unadapted path.
Preferring an unachievable path controlled by an automatism over adapted manual control of a visual, stable and powerless short final demonstrates the existence of such reluctance.
Using mixed manual and automatic inputs isn't a good idea. If you loose AP take manual thrust control and vice versa.