It means that there are qualities or facts about someone or something that make them more complex, better or worse than you would think having just a minimal knowledge of he, she, them or it.
If something "meets the eye", that means that it is seen.
It can have a positive or negative flavor.
"He doesn't seem too intelligent at first, but there's more to him than meets the eye. He is actually a rocket scientist."
"It looks like just an accident, but there is more here than meets the eye. I think the fire was set on purpose."