This question has been posed since before the time of Christ, most famously by Epicurus. You've mentioned the Holocaust, but that is pretty easy to get around by simply citing free will as some have done here.
What's not so easy to get around are the existence of natural disasters. What kind of God would allow an innocent child to suffer while simultaneously allowing evil men to prosper? To simply say that "God works in mysterious ways" is a cop-out. Invoking Karma leads to many problems as well.
The only real way to get around this problem while still holding to a belief that God exists is to modify the usual definition of God, most commonly by changing the definition of what it means to be "all-good" or "all-powerful".
You can hold onto the possibility of a "clockmaker" God, but as you say, there's really no point in it if God is uninterested anyway.
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