Romans 1:18
“For the wrath of God is revealed from heaven against all ungodliness and unrighteousness of men who suppress the truth in unrighteousness.”
"Why!?" is a perfectly valid question for Habakkuk to ask. It demonstrates that he cannot reconcile bad events with a good God. Wrestling with the problem of evil is common among those who experience it's destruction. If God is good, why does tragedy happen? If God is good, why does evil win? How can I look at the mess around me and conclude that God is in control, much less cares?
These are reasonable questions and good questions. They are not questions about why God would judge a sinful nation or individual. I suggest that Habakkuk is too insistent and the situation too dire for such an explanation. A faith-filled believer doesn't need God to explain punishment for sin. Few people need God to explain why He punishes sin. Cause and effect is not the issue in Habakkuk's introductory questions. Divinity and simultaneous evil is the question being asked. Habakkuk is questioning how a loving sovereign God and obvious profound evil can co-exist? "It shouldn’t be this way, this makes no sense, you God need to answer, and answer well why this evil has occurred!" We see a hybrid of this question repeated later in the chapter at verse 13.
Not all bad things that happen are a result of judgement. The Chaldeans storming the city does not have to be because Judah's people have sinned. Calamity comes because it is the natural state of the fallen world. Tragedy may well be a product of The Fall (Gen 3) but that does not necessitate that the Chaldeans are the result of Judah's moral failure. Rather tragedy comes because it is the natural state of our existence. We will see in God's responses that Habakkuk has a few errant beliefs. God is going to correct Habakkuk later. Here we see Habakkuk’s first of several misunderstandings.
Habakkuk bears the assumption that God's design and management of the cosmos is solid and sure. There is no reason or faithlessness that would or could change the grand orchestration of existence. Therefore, in Habakkuk’s mind he questions how it is that such evil could occur in a cosmos designed and managed by God? If God is the root of all things, keeping the very planets and our small lives in sequence according to His will, how is it that evil then occurs?
The evil that happens in tragedy is more than a consequence, it is a state of being. Evil happens because this existence we navigate is inherently flawed, and God is well aware of that fact. Indeed, He is so aware of that fact, that He chose to intervene on our behalf and secure a path out of this broken place. God owned this broken reality at the cross. That is how much He cared about what happened. We are prisoners in a broken existence, scourged with the whip of tragedy and He said He will not stand for it. So He owned it.