The plain sight thing has always bugged me too, but assuming it was the flashlight - and the nature of the injury and the lack of prints leads me to believe it was - they had only a few choices.
They could have hidden it in that huge messy house. But they risked LE finding it and connecting it to the head injury. Why would a intruder bother to find a hiding spot in the house for the murder weapon?
They could have tried to dispose of it, but it was a heavy object, and it probably would have been much more difficult to dispose of than some tape or string, especially with the clock ticking that night.
They could have left it where the head strike happened, but this would have potentially left clues they didn't want left behind. And this would have confirmed without question that it was the weapon used.
Without actually hiding it, they could have put it in a kitchen drawer or cabinet. But, assuming the cops figured it was the weapon, why would an intruder bother doing this? (Although he was nice enough to put Patsy's pen and pad neatly away, so maybe this would have worked.)
They may have figured leaving it print-less on the counter was the safest, most neutral option of all. Not hidden, not put away, not randomly tossed where the head strike occurred. If the cops determined it was the murder weapon, it could have just been where the murderer put it down. Or maybe they wouldn't connect it at all. Whatever the reasoning, it worked for the Ramseys.