I definitely think that if he'd said "good atheists" that would've put a different spin on it. This didn't seem like he was trying to make a huge announcement, so maybe it's wrong to read too much in to it, but I can think of a couple ways to take this:

• A "good" atheist is more moral than a hypocritical Catholic
• A hypocritical Catholic makes Catholics look bad, if they're going to do immoral things it's better that they be atheists so they don't make us look bad
• Being a good Catholic is such a high moral standard that someone acting the opposite of that is terrible, and would even be worse than an atheist.

Some of those are a pretty cynical way of taking it, but again, it was something the Pope was saying that other people said, and people might've meant it as something of a backhanded compliment? Personally I think when he said that "atheists as good people if they do good" was an important point to make, and this headline is probably going to get more attention than it really deserves just because it can be taken in a controversial way.