The actual text of the pope's sermon (translated into English) is here:
I had to copy it over into a word processor to read it, since the text chosen was so small.
Anyway, the theme is the journey of the Wise men from the East (the Epiphany story, whose annual celebration is January 6, the day of the sermon),
combined with the consecration of four new bishops (a recent Epiphany tradition).
It is unclear why the Pope chose to describe a dominant mindset of parts of the contemporary world as "agnostic," except that that does seem to echo
his conception of the Wise Men:
These men who set out towards the unknown were, in any event, men with a restless heart. Men driven by a restless quest for God and the salvation
of the world... But they desired more than simply knowledge about things. They wanted above all else to know what is essential. They wanted to know
how we succeed in being human. And therefore they wanted to know if God exists, and where and how he exists. Whether he is concerned about us and how
we can encounter him. Nor did they want just to know. They wanted to understand the truth about ourselves and about God and the world... They were men
who sought God and were ultimately on the way towards him. They were seekers after God.
So, perhaps "agnostic" is a good description of the Wise Men's mindset. Perhaps, too, the Pope is expressing optimistism that actual rejection of
him, and the approach to God which he represents, isn't as settled as "atheism" would connote. Ironic, if so, to condemn the intolerance of what is
almost necessarily a tolerant stance.
Here are his remarks about agnosticism, in the context of advice to the new bishops.
How can we not think, in this context, of the task of a Bishop in our own time? The humility of faith, of sharing the faith of the Church of
every age, will constantly be in conflict with the prevailing wisdom of those who cling to what seems certain. Anyone who lives and proclaims the
faith of the Church is on many points out of step with the prevalent way of thinking, even in our own day. Today’s regnant agnosticism has its own
dogmas and is extremely intolerant regarding anything that would question it and the criteria it employs. Therefore the courage to contradict the
prevailing mindset is particularly urgent for a Bishop today. He must be courageous. And this courage or forcefulness does not consist in striking out
or in acting aggressively, but rather in allowing oneself to be struck and to be steadfast before the principles of the prevalent way of thinking. The
courage to stand firm in the truth is unavoidably demanded of those whom the Lord sends like sheep among wolves. “Those who fear the Lord will not
be timid”, says the Book of Sirach (34:16). The fear of God frees us from the fear of men. It liberates.
I am an agnostic. Would that my view of things were "regnant" or "prevailing." In truth, agnosticism is a minority view, hemmed in from both
sides, by believers and by the insistent rejectors of belief. I know no "dogma" of agnosticism, and feel no intolerance, much less extreme
intolerance, toward those who "question it," which would be almost everybody (including agnostics, who typically question ourselves quite
I speculate that the Pope meant some variety of "secularism," and called it "agnostic" to be diplomatic. In any case, the Pope doesn't specify
any particular aspects of this supposedly prevailing mindset for special attention. So, Dr Berry's speculations (in the article linked in the OP,
which is largely her, and very little of fresh Pope Benedict, despite the headline) about gay marriage, the ordination of women or "attempts to push
religion out of public conversation" are her concerns, and not necessarily what he had in mind.