Yes, atheists can be libertarians. There are atheist libertarians, Christian libertarians, Muslim libertarians, Hindu libertarians, Jewish libertarians, Buddhist libertarians and so on.
The philosophy of libertarianism has a set of core values, including personal liberty and non-aggression, that are compatible with atheism and most organized religions.
Atheism has no defined moral or religious positions. Atheism is the belief that the universe was forged by means independent from divine creation. While atheist scientists, astrophysicists and philosophers have various theories on how the universe was created, there is no unanimous intellectual consensus.
Therefore, atheism is compatible not only with libertarianism but virtually any political philosophy: libertarianism, socialism, communism, fascism, republicanism, liberalism, anarchism etc.
Many undecided libertarians adhere to agnosticism, claiming that insufficient data and the lack of human intellectual capacity make it impossible to define objective truth concerning how the universe came into existence.
Other libertarians subscribe to deism, asserting that God created the universe and everything in it but chose not to interact with human beings. Freethinker Voltaire and individualist anarchist Lysander Spooner were deists.
Some libertarians hold theistic views but, criticizing the structure and historical authoritarianism of the church, embrace secularism and call themselves "irreligious."
Many famous libertarian and objectivist writers, philosophers and intellectuals have proclaimed their atheism or agnosticism, including Ayn Rand, Henry Mencken, Murray Rothbard, Penn Jillette and Milton Friedman.
For more information on libertarianism, see our Ultimate Guide to Libertarianism