Pope Benedict XVI has often sympathized with those at different places on the journey of faith, including those who struggle to believe in God or don't believe at all.  Two examples come to mind.

In his outstanding Introduction to Christianity, then-Fr. Ratzinger wrote powerfully of the forces that can threaten faith. The believer and unbeliever, wrote Ratzinger, are connected in their vulnerability. Each one of them, he said, must ultimately acknowledge that no belief system, religious or otherwise, can completely shut itself off from influences which might undermine it. That vulnerability is the starting point for dialogue.  

In Porta Fidei, his apostolic letter announcing the Year of Faith, Benedict wrote that "we must not forget that in our cultural context, very many people, while not claiming to have the gift of faith, are nevertheless sincerely searching for the ultimate meaning and definitive truth of their lives and of the world. This search is an authentic 'preamble' to the faith, because it guides people onto the path that leads to the mystery of God."

In retirement, Pope Benedict has kept that same sympathy. A letter from Benedict to Cardinal Bertone has recently been published in which the Pope Emeritus writes eloquently of the Church's universal mission. See this story from the Catholic News Agency for more.