From The Washington Post (2007):
A study released in June by the Barna Group, a religious polling firm, found that about 5 million adults in the United States call themselves atheists. The number rises to about 20 million -- about one in every 11 Americans -- if people who say they have no religious faith or are agnostic (they doubt the existence of a God or a supreme deity) are included.
So among the adult population the correct proportion as of 2007 was 2.2% atheist, 9.1% non-religious.
As to whether atheists are over or under represented in prison, I can't say, but I don't see how this matters anyway.
1a) Atheists might be over represented because being irreligious in a predominantly religious country, they are treated unfairly by juries.
1b) Atheists might be over represented because they are bad people who commit more crimes.
2a) Atheists might be under represented because they tend to be better educated, hence more able to handle questioning well, afford better lawyers, etc.
2b) Atheists might be under represented because they are good people who commit less crimes.
The religious make-up of prisons isn't evidence of anything really. Correlation not indicating causation and all that.
