In Milton's Il Penseroso, published in 1642, the following lines appear...
"Of forests and inchantments drear
Where more is meant than meets the ear."
So there is the earliest recorded use of the idea of something meeting a human organ.
P Paxton's Stray Yankee in Texas, published in 1853 has...
"There might be more in it than at first met the eye."
And that appears to be the earliest use of 'eye' in the same sort of context.
All the saying means, of course, is that outer appearances are not always reliable for forming a judgment. Perhaps you think the person is really better than he appears, but it could just as easily mean the opposite.