The answer to this question has already been answered by an online Catholic news article, discussing this subject with the exact phrase, "just be good", in it. Upon close examination of the news article, the newswriter/blogger/journalist suggests:
The Holy Father is full of surprises, born of true and faithful
humility. On Wednesday he declared that all people, not just
Catholics, are redeemed through Jesus, even atheists.
However, he did emphasize there was a catch. Those people must still
do good. In fact, it is in doing good that they are led to the One who
is the Source of all that is good. In essence he simply restated the
hope of the Church that all come to know God, through His Son Jesus
Additionally, it is said in the article that fact that atheists are led to Jesus Christ - the source of all good - is recited during Good Friday in the form of a prayer. So, Pope Francis may not really be adding anything new.
The disciples, Pope Francis explained, "were a little intolerant,"
closed off by the idea of possessing the truth, convinced that "those
who do not have the truth, cannot do good." "This was wrong... Jesus
broadens the horizon." Pope Francis said, "The root of this
possibility of doing good - that we all have - is in creation."
The Catechism of the Catholic Church explains that "Since it rejects
or denies the existence of God, atheism is a sin against the virtue of
religion but the imputability of the offense can be significantly
diminished in virtue of the intentions and the circumstances"
So, although the atheist by that definition has sinned against God by denying or rejecting God, he or she may still perform good deeds in the world, and those good deeds will eventually lead him to Jesus Christ, time not specified. I think it's trying to say that good works and good faith come hand in hand. So, if an atheist expresses good works but claims not to have faith in Jesus Christ or God, then somehow the good works will lead him to faith. Therefore, to answer your question, Pope Francis presumably told atheists to "just be good" as a way to evangelize them and call them to Christ.