According to news reports this is what Pope Francis actually said:
The Lord has redeemed all of us, all of us, with the Blood of Christ: all of us, not just Catholics. Everyone! 'Father, the atheists?' Even the atheists. Everyone! And this Blood makes us children of God of the first class. We are created children in the likeness of God and the Blood of Christ has redeemed us all. And we all have a duty to do good. And this commandment for everyone to do good, I think, is a beautiful path towards peace. If we, each doing our own part, if we do good to others, if we meet there, doing good, and we go slowly, gently, little by little, we will make that culture of encounter: We need that so much. We must meet one another doing good. 'But I don't believe, Father, I am an atheist!' But do good: We will meet one another there.
Jesus clearly died for all people. Everyone has the opportunity to receive the gift of salvation through Jesus Christ. However, not everyone fully knows or understands this. In such cases the Church has traditionally referred to such individuals as invincibly ignorant. Such individuals who, through no fault of their own, do not know or understand the fullness of salvation offered by Christ through the Church are still expected to responded to God and His grace as they are able to know and understand it. For the atheist that would mean following their conscience and doing good since that is the only area of overlap they would have with people of faith. It is not that their good works earn them salvation, but that they have responded to God's grace in the only way that they could. This can be seen in the Church's Good Friday prayers:
Let us pray
For those who do not believe in God,
that they may find Him
By sincerely following all that is right.
Ultimately the Holy Father's main point was not eschatological but about cooperation amongst peoples to build a better world:
"They complain,” the Pope said in his homily, because they say, “If he is not one of us, he cannot do good. If he is not of our party, he cannot do good.” And Jesus corrects them: “Do not hinder him, he says, let him do good.” The disciples, Pope Francis explains, “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”