When injustice is done on earth, when the kingdom of evil takes control and stifles the righteous and the innocent, it is only natural for a person to ask G-d, "Where are You?" In a period of Divine concealment, doubt and heresy burgeon fourth, as it says
(Deut. 31:17), "I wil hide My face from them, and they shall be devoured. Many evils and troubles shall come upon them, so that they will say on that day, 'Are not these evils come upon us because our G-d is not among us?"
Indeed, many Jews who saw the atrocities of Holocaust ceased to be religious. They thought that if G-d really exists, how could He let all this evil happen to His people?
Actually, there is no contradiction. G-d warns Jews in the fifth book of Moses what will happen to them if they rebel against Him. G-d as well says that if they follow His will they'll live a happy life.
G-d is just and doesn't punish immediately. He gives the opportunity to repent and return to the righteous path. Also, His punishments are proportionate to the sins.
Numerous Jews in Europe wanted to assimilate, to cease to be Jews. They did their best to show themselves and their children that they are now "civilized enlightened" Europeans and "dark primitive" Judaism is the matter of the past. Many not only stopped to practice Judaism but also were ashamed to be Jewish and tried to conceal it by all the ways possible. Instead of being G-d's people, as G-d Himself commanded, they tried to run away..
But this is the false path. G-d created the world in such a way that the Jews ARE destined to be different. Nothing can change it. And if the Jews themselves try to deny it, G-d brings on them tyrants like Hitler who remind it to us..
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P.S. "different" doesn't mean "superior" or "inferior", as antisemites of different types say. Just - different.
הן עם לבדד ישכן ובגוים לא יתחשב
Behold, a people who dwells apart, And will not be reckoned among the nations.(Numbers 23:9)