By & large, most of the smart kids at my school were not popular. There were a few who were well-liked by most, regardless of their clique, which technically is popular, but they weren't a part of the "in-crowd" (which is what I assume most mean when they say popular).
I personally did well in school academically, but I was not popular because 1) I didn't care & so I made no effort to befriend people, and 2) I was a loner, and 3) I had an odd/cold demeanor that put people off a bit. I wasn't teased though, just mostly ignored & forgotten, which is what I think I wanted. Occasionally I saw the eyes roll or heard a snicker when I got the highest test score in the class yet again, but I took that to be resentment more than mocking.
Of course, there was the over-achiever crowd who were not nerds & were well-known, but they were still seen as a bit nerdy by the in-crowd types.
Not to pull the "jealousy" card, but to a degree, I think some kids resent the smart kids, as school comes easily to them, and so they seek to pull them down to their level by nitpicking what seems inferior about them (their appearance, their ability to socialize, etc). In a similar vein, the typical nerd may dismiss those types as dumb jocks (or whatever), seeking to devalue their strengths to make their own seem superior.