Viking, perhaps it has to do with the 'ergonomics' of cockpit structure.
When you see the 109, the flap crank-wheel is on the left side, like a large windmill on the side of the cockpit. I have no real idea on what the combat conditions would be like, but it doesn't seem too difficult for the pilot at a HOTAS position, to slip his left hand back, feel the wheel, and then crank it a few degrees as he wants.
But I'm not sure how easy it would be if the lever was a part of the frontal/curved instrument board. The pilot would have to take his eyes off from his target, stretch his hand to the frontal board, use his fingers to move the lever to one side, and then move the lever again to a "Stop Valve" position, do his maneuver, and then retract the flap again when its not needed... while the switch/lever looks much more "modern" than the mundane "crank wheel", I'm guessing the crude "wheel" approach might actually be more easier for the pilot to get his hand on during intense combat.
Besides, it isn't uncommon for the average pilots to make all sorts of mistakes... especially rookies, in the heat of the battle, are known to pull wrong levers, put switches in wrong positions, turn something on and then forget about it.. and etc etc.. so I'm guessing flap usage in combat, wasn't something an airforce commander would want to intentionally teach to the pilots under his wing. Perhaps some pilots who fly regularly with slick veterans might be influenced to use flaps on a more regular level, but I really don't see a rookie pilot doing that.
Like, for instance, the story of Lawrence Thompson and his P-51... although his claims of meeting Hartmann is widely disputed, during that combat with the 109 he pulled down the flaps, and then actually forgot to retract them - which caused his plane to fall into a lucky stall/spin, which saved his life.
Ofcourse, this is a mere guess.