Every neuroscientist I know HATES that saying.
My favorite historical explanation during grad school was that when neurology was getting started (late 1800s), it got a big boost during the Russo-Japanese War, because the higher velocity bullets meant that more and more soldiers started surviving head wounds. Those early neurologists quickly mapped out the sensory and motor cortices by the obvious blindness or paralysis following damage to those areas. But the deficits from the higher level association cortices (which are most of the cortex) were much more subtle. They called these 'silent' cortex because they didn't appear to do anything. And the myth was born.
Interesting theory. I was assuming it was because 90% of the brain is used for functions that don't include surface thoughts, and idiots interpreted this as 'people only use 10% of their brain!'