Which of these sentences is correct?

Neither one. First of all, atheism was not a part of the Nazi philosophy, and I don't think real Christianity is a part of the KKK, despite what they might think. But even if both were correct in the first part, you cannot judge an entire group by only some of the members of that group.

Neither is correct.

For the second one, at least the members of the KKK do actually tend to self-identify as Christian. For the first one, even that part isn't true. Nazis didn't call themselves atheists, they called themselves Christians. They put atheists into camps.

Perhaps it should say:

* Nazis persecuted atheists, therefore atheism is good.

Neither, nazism wasn't even atheistic, most nazi's were part of some branch of Christianity and had "God with us" written on their belt buckles.

And KKK is just a small extremist group that doesn't represent

anyone but themselves.

Neither.

A subset of a group does not determine qualities associated with the entire group.

i.e. bananas are fruits therefore fruits are yellow.

This is not a correct conclusion. SOME fruits are yellow is correct.

Some atheists and some Christians are evil is correct.

Neither.

They are both extremist groups, and not representative of the wider ideas of either Christianity or atheism.

KKK is not Christian. Nazism is only an example of some atheists at their worst.

Neither.

Neither are correct.

God Bless

Perhaps the second, yet there are radicals in every group.

Nazism is not atheistic. It is anti-semitic. There's a difference.

Neither, generalizing is stupid.