We all have an instinctive feel of disgust for Holocaust deniers. RIGHTFULLY SO!!! People deny the Holocaust not b/c there is a shred of evidence to support their preposterous claim - there are millions of pieces of evidence to refute it. People deny the Holocaust b/c they are rotten, evil anti-semites. We have zero tolerance policy for such people - and that is correct.
However, we tolerate people who deny the existence of G-d. Why is that?? The world was not created so that people acknowledge the Holocaust but rather that people recognize Hashem. So we should equally [or more so] have zero tolerance for heretics. I think one reason is that for us - the Holocaust is real. Hashem is much more of an abstract concept. The reality is that Hashem is more real than anything that exists. The Avodah is to live that reality.
Another reason we tolerate atheists is that we live in a pluralistic society. We are trained to think that just about any opinion or philosophy is valid. So one may believe that it is fully OK to crush to death an innocent fetus b/c the mother is not in the mood to have a baby. One may think that is is perfectly OK for a man to marry another man. One may think that whether a Jew keeps Shabbos and how they keep Shabbos is a matter of personal taste.
The fact is that as believing Jews, we maintain that there is objective truth. Within a certain spectrum there is room for differing opinions [such as Beis Shammai and Beis Hillel, the followers of the Baal Shem Tov and the followers of the Vilna Gaon etc.] but beyond that spectrum false beliefs should be anathema to us. PARTICULARLY atheism and its derivatives.
Let us NOT be swept away with the spirit of liberalism and moral relativism that is overtaking the world.