Many people would agree that bugs in general are not cute. Lots of folks, in fact, find them gross, whether we're talking about flies, cockroaches or ants. (And we know "bug" is not a scientific term for an insect, but we're dealing with a simile here). So could such creepy critters have cute ears? Highly unlikely. But more to the point, bugs don't generally have ears. At least not the kind of ears we think about -- those two appendages on either side of, or on top of, the head. Grasshoppers have ears on their abdomens, for example, while katydids sport them on their front legs. Lacewings? Their ears are on their wings [source: University of Colorado Boulder].
So where did the saying come from? Possibly from the word "acute," meaning sharp or keen. Bugs have acute hearing; they can detect faint sounds, plus those that are high-pitched. In 18th-century England, "cute" was another word for "acute." Perhaps people back then described insects' hearing, or ears, as "cute," meaning they were really good at their job, not adorable [source: Martin].