I wanna see the Force lightning, damn it!

In an episode of their show Bullshit, Penn and Teller argue that members of PETA are like Nazis. They list similarities between PETA and Nazis. They show pictures of PETA rallies alongside pictures of Nazi rallies to show that PETA protesters look a lot like Nazis. They point out, of course, that Hitler was a vegetarian.
Obviously, they go on to state, they aren't equating PETA with Nazis. They're using the argument to demonstrate that anyone can site similarities between their ideological opponents and Nazis. They're using the argument to point out that comparing one's opponents to Nazis is utter Bullshit.
I'm guessing the Pope doesn't watch Bullshit; which isn't his fault, they probably don't get Showtime at the Vatican. 
People who take the side of the Pope, who are growing fewer and far between, argue that the Pope isn't comparing atheists to Nazis when he says:

Even in our own lifetimes we can recall how Britain and her leaders stood against a Nazi tyranny that wished to eradicate God from society and denied our common humanity to many, especially the Jews, who were thought unfit to live. As we reflect on the sobering lessons of atheist extremism of the 20th century, let us never forget how the exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus a reductive vision of a person and his destiny.

Maybe there's something going over my head, but making the very false claim that the Nazis were atheists who tried to "eradicate God from society" and then stating that it was "extreme atheism" that was to blame seems just a bit similar to comparing atheists to Nazis. Even though Hitler said in a 1933 speech:

We were convinced that the people need and require this faith. We have therefore undertaken the fight against the atheistic movement, and that not merely with a few theoretical declarations: we have stamped it out.

I've heard other folks claim that saying things like "Obama is in favor of socialized medicine. The Nazis were in favor of socialized medicine as well," is not comparing Obama to Nazis. Maybe it depends what your definition of is is.

So here's the new rule, cats and kittens. Just stop comparing people to Nazis. Stop doing it overtly, and stop doing it with coy implication - you're not fooling anyone, you're simply showing you don't have the courage of your convictions.

Republicans aren't like Nazis, Democrats aren't like Nazis, even the KKK aren't like Nazis - although they do share some of the ideology. Only Nazis are like Nazis. The Third Reich was dedicated solely to the cause of evil, to the cause of murder, torture, and hatred. Do not cheapen, do not disrespect, do not trivialize the incredible, the unholy acts performed upon the victims of the Nazis by making comparisons, coy or otherwise.

I do not, however, have any problem with this comparison. Although I suppose it's disrespectful to the people of Alderaan.

By the way, a great, great many Catholic individuals risked unimaginable torture and grueling death to try and save others from the Nazis. Like this guy. I know first-hand, that Catholics can be some of the most ardent, most loving advocates of peace and love. These Catholics deserve a far, far better leader.