It was belief that caused the holocaust, a belief that Jews (read Christ killers), and homosexuals (another bible driven phobia), were the cause of Germany's woes and so had to be wiped out. The belief in God persists even now.
I think you are overly simplifying the situation. The initial cause of tension between Jews and Christians wasn't based on the idea of Jews being Christ killers in the first place.
Jews were a minority. As history has shown, minorities are hated. If the Jews had made up a majority, or even an equal population, they would not have been the scape goat. Some other minority would have been. Which is why it wasn't just Bible driven phobias or hatreds that were persecuted during the Holocaust. To try to make this into a religious thing simply does nothing to help the situation, and certainly ignores the evidence that we have.
As for why God didn't do anything to save the Jews during this harsh and brutal outcome, one has to look back at the history of the people. This is not the first time that the Jews faced massive persecution. The OT is filled with it. After Egypt, they finally gained their promised land. After Joshua and the Elders had passed away, we see turmoil. The Jews do evil, God gives them over to plunderers, the Jews cry out to God for help, God sends a deliverer or a Judge to save them. We see this pattern occur some 12 times.
After that, the Jews gain a King, and are relatively okay. Solomon dies, the kingdom splits, and we start to see the pattern happen again. The North Kingdom first, commits evil in the eyes of God, and is latter destroyed by the Assyrians. Next, the Southern Kingdom commits evil, and then is dispersed by the Babylonians. So there is a definite pattern here of the Jews being persecuted.
And as seen, at one point, it was thought that the persecution came from committing evil in the eyes of God. It was because of the sins of the ancestors that the Jews suffered. Later, we start seeing a new idea evolve. Ezekiel is a good example of this. The new idea is that it wasn't because of the sins of their parents that they suffered, but that everyone is responsible for their own sin. The key is that one has to turn away from their transgressions and then they will live. And that God is just, and they will eventually be restored.
It was out of this idea, that God was a just god, that the apocalyptic idea arose to explain the persecution and misery that some Jews had faced. Even though they may suffer in this time, they will be repaid when the Kingdom of God is set up here on Earth.
Both of these ideas still persist to this day. However, there are also many other reasons as well. Some Jews claim that the Holocaust was a sign of the breaking of the covenant, and we are now in a time a free acceptance of the Covenant.
Another explanation I've seen is that God is not actually omniscient or omnipotent. So he couldn't have stopped what was happening, and didn't know it would happen.
Yet another explanation is that since God allows free will, bad things are naturally going to happen.
Basically, there isn't just one answer. There are many different answers. It is similar to the many answers there are to why God would allow bad things to happen.