Being an atheist doesn't make anyone more intelligent, at least not measurably, but being more intelligent increases the likelihood of being one.
"The authors investigated the link between religiosity and intelligence on a country level. Among the sample of 137 countries, only 23 (17%) had more than 20% of atheists, which constituted “virtually all... higher IQ countries.” The authors reported a correlation of 0.60 between atheism rates and level of intelligence, which was determined to be “highly statistically significant”."

http://en.wikipedia.org/wiki/Religiosity_and_intelligence#Studies_comparing_religious_belief_and_IQ