In all their affliction he was afflicted (Isaiah 63:9; ESV)
A common reason given by atheists for their rejection of God (at least of the God of the Bible) is the problem of evil. "How can a good God allow suffering?" they say. This indeed is a difficult question and one that the Bible itself asks in the books of Job and Habakkuk in particular as well as several of the Psalms. For many Jewish people today, the Holocaust was final and absolute proof that God is a myth. I would guess that those who are embittered against the biblical God would not find most of the Bible's handling of this issue intellectually satisfying. One reason for that is the Bible doesn't provide us with a logical, philosophical treatise of the problem of evil.
Instead of an intellectual answer, the Bible gives us something a whole lot better: a relational one. Our short quote from the prophet Isaiah is a good example: "In all their affliction he was afflicted" (Isaiah 63:9; ESV). God through the prophet asserts that he himself suffered as Israel suffered. This is something far more than a sentimental thought about a supreme being who empathizes from afar as if a realization that God "understands" should somehow make us feel better about tragedy, injustice, and suffering. God really does feel our pain.
But then why doesn't he do something about it? He is the all-powerful God, isn't he? I will try to answer that question. But first, there is a misguided common assumption about God and his power that gets in the way of the truth of the matter. Many of us, even the atheists among us, expect God to behave like a superhero. Most superhero characters and stories are rather flat. I know their personalities and adventures can be complex. But at its core, their stories are very simple. People are in crisis; the superheroes save the day. It's always the same: evil threat is eventually thwarted until the next evil threat rears its head.
This is how we tend to expect God to resolve evil. But because he doesn't, we reject his existence. Why doesn't he behave like a typical superhero? If the God of the Bible is real, he should make Superman and friends look like wimps. Shouldn't a real God outclass the fake ones?
But if God dealt with evil according to these expectations, he would break the universe. This type of intervention wouldn't resolve the problem of evil, it would undermine life altogether.
Life as created by God is more complex and wonderful than anything we can imagine. This is one of the reasons why evil and suffering are as bad as they are. The depths of the problem of evil are not as simple as the threat of some supervillan trying to take over or destroy the world. The Bible teaches that the curse that was a result of our first parents' disobedience to God, pervades the whole creation through and through. The resolution of this, the greatest of all problems, requires God himself to experience firsthand the effects of that curse in order to undo it.
The greatest expression of "In all their affliction he was afflicted" was experienced by God in the person of the Messiah when Yeshua took on the curse's effects by his unjust execution. Isaiah's words suggest that this was not the only time God shared our sufferings. In ways we don't understand, he was intimately affected by his people's plight. We need to realize that we are not in this alone. He who designed life with all its complexities, suffers with us. We are in this together.