The Pope has decided that forgiven doesn't mean forgotten. When he recently un-excommunicated some dissenters, and they continued to spew hateful, anti-semitic Holocaust-denial, the Pope's silence implied consent. He is silent no more. That isn't to say he has re-excommunicated the offender, but he has called him out. It's a start.
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The comment that has stirred up the most condemnation from the press is Richard Dawkins' mention of "Pope…Nazi," which everyone assumes was about the current Pope. Wrong. Everyone knows the current Pope is most properly addressed as "Pope Palpatine".
You've gotta see this amusing post from Gribbit about Pope Benedict and his now-infamous statement about Islam being spread by the sword. He says the Pope shouldn't have to apologize for his remarks, which I agree with.
The Pope has said while in Africa that condoms may increase AIDS problems. What? He is so insulated from science that even the most basic application of science to our problems eludes his comprehension.
I'm not sure it's really the case that the Pope is calling him out, more that he hoped no-one would notice but noe the storm has kicked up he has to be seen to be doing something. Do you really think the Pope never knew about the bishop's specific remarks and viewpoints prior to the unexcommunication (recommunication?), given that he was actually on television airing his ignorance? Is he actually that careless?
So much for the doctrine of papal infallibility. ;)