I have given this topic a lot of thought since I go to a good, academically rigorous university and here the chicks are generally lacking in the physical beauty department.
Without venturing into the realm of actually defining intelligence (I think we can all point out a stupid chick when we see one), I would definetely say that smarter chicks tend to be not as attractive. And I am not talking about IQ or booksmarts or any specific facet of intelligence, rather intelligence as a whole concept that encompasses all these things.
There are several theories which I have come across...
First theory: This could be a statistical thing. Statistically, there are not as many intelligent people as stupid ones. Thus, to come across someone who is intelligent and attractive is even rarer. And, by comparison, the attractive girls you run into are not generally intelligent because intelligence is rare.
Second theory: intelligent people do not care as much about their looks, and thus let their appearances slide. I personally think this is bs.
Third theory: it is not socially cool to be perceived as too intelligent because it makes the morons feel self-conscious about their own abilities and they hate you for it. Thus, those chicks who try to fit in with certain social groups who value physical appearance subjugate their own intelligence. They pretend not to know as much as they do, affect mannerisms of the stupid people they hang around with, stop learning on their own and seeking out new experiences, and, in sort, become stupid because they stunt their own intellectual growth.
I know people (guys and girls) who have gone this route. It's kinda sad because these people waste their own potential for self-improvement solely to ascribe to a social group that glorifies stupidity.
Fourth theory: what bishopdonjuan said, namely pretty girls don't have to rely on their intelligence.
I have noticed that cute girls (as opposed to hella fine girls) have a lot more game. They are better flirters, more socially apt, and generally know what they are doing when it comes to picking up men. Fine girls, in my experience, have no skills in this area, relying primarily on their looks to get dates.
Fifth theory: IT IS ONE BIG FVCKING COSMIC JOKE. This is the theory that I have picked because, really, there is nothing you can do about it except deal with it.
Oh yeah, and by the way, I bet the opposite idea is true as well, namely attractive intelligent men are hard to find.
Peace.