Bullies pick on ANYONE they can, for whatever reason they can. They bully the smart, the not-so-smart, the pretty, the ugly - anyone they think who can't stand up for themselves, or anyone who attracts attention for being different.
In my school there were plenty of smart people who were not bullied - why? Because they were also tall and pretty gosh-darn athletic. Some smart people were bullied, but that was usually because they looked like they could be.
I hate to say it, but with some people you can just tell, with one, glance: yep, they'll be bullied. If they are quiet, soft-spoken, and they aren't built like a truck, chances are some bully will try to pick on them. Usually, smart people who focus on academic work are soft-spoken, quiet and unfit - that is one of the reasons why they are mostly picked on.
Also, academically gifted students can tend to lord their skills over the students who are not so good at academic work. One student in particular in my 10th grade mathematics class was pretty good at math, and would derisively refer to anyone who wasn't as a "slow-boy" or "slow-girl". He wasn't too popular after that. It's a myth that all the athletes are all the bullies - I've met enough academic bullies both during school and after - they just tend to use passive-aggressive behaviour, trash-talking, rumours and sabotage to bully their victims.
Also, people who do well at school academically also tend to behave better in class. Bullies hate rule-followers for a reason I could never quite understand.
But by and large, bullying is not due to how intelligent someone is - it's due to how easy a target they are perceived to be. I've seen bullies pick on the smart kids by calling them "egg-heads", "squares" or what have you, but then turn around and pick on the learning-disabled kids by calling them "Retards" "dumb-asses" or "morons" or what have you. A bully will pick on ANYONE who is 1) Perceived to be an easy target and 2) Different enough from themselves to find insults for.