By equating Nazism with atheism the Pope is making two fundamental errors which are really not very becoming of someone with his academic credentials and knowledge of German history.
1. He is suggesting that Nazism in Germany developed from atheism. However, Germany was a very Christian country in the 1930's and the Nazis themselves had quite strong religious beliefs. Not necessarily a belief in the Christian God, but the SS had a strong belief in destiny and being guided by a higher power. Hitler himself was a Roman Catholic, never renounced his church membership and used it to suggest that God was on the side of the German people. You can read more about this here: was Adolph Hitler an Atheist.
2. He is suggesting that people can choose to believe. In other words if all those atheists just chose to believe then the world would be a better place. As a theologian Pope Benedict should realise that faith is a gift. People either believe or they do not. Their state of belief may change with time, but the suggestion that an atheist can choose to believe in God is flawed. Atheists are asking for evidence for the existence of God. Atheists want to be true believers, not just people who go along with it for the sake of it. The nature of their scepticism is that if sufficient evidence comes forward then it may be evidence for some other God and not the Christian one. I don't think the Pope is in favour of that sort of open minded seeking of God.
The only explanation I can put forward for the Pope's statement is that he is using coded language. If we substitute "non catholic" for "atheist" it makes more sense. If the Nazi leaders had stayed true to their catholic faith then they would not have done all those terrible things. A Christian can choose to become a Roman Catholic. Their belief in God and Christian faith is already set. In the same way if all atheists choose to become Catholics then we will have a united and peaceful world. It might well produce a social unity, but it would not be people who truly believed.
I don't think the Pope really wants to engage with the issue of faith and atheism. If he did he might be in a better position to add something than any of his recent predecessors, but his concerns seem to be more for the integrity and growth of the Roman Catholic church.