"'they all come bent on violence. Their hordes advance like a desert wind and gather prisoners like sand. They deride kings and scoff at rulers. They laugh at all fortified cities; they build earthen ramps and capture them. Then they sweep past like the wind and go on - guilty men, whose own strength is their god.'" NIV translation
The Babylonians thought of themselves as being unstoppable. This passage describes them as a desert sandstorm and if you have been in one of those you can appreciate what is being said. These sandstorms are caused by the wind picking up sand and there can be such a great cloud of sand that it actually gets dark in the middle of the day. These people are guilty of idolatry in that they think of themselves as gods. This is much the same attitude as many people today as they trust in their own efforts and strength.
"O Lord, are you not from everlasting? My God, my Holy One, we will not die. O Lord, you have appointed them to execute judgement; O Rock, you have ordained them to punish. Your eyes are too pure to look on evil; you cannot tolerate wrong. Why then do you tolerate the treacherous? Why are you silent while the wicked swallow up those more righteous than themselves?" NIV translation
Habakkuk acknowledges who God is and the fact that He is just in bringing judgment on His people. (God answered his first complaint by telling him that He was going to use the Babylonians to conquer His people.)
Now, the prophet is not happy with God's choice of instruments as he basically tells God that they are even worse than the people they are going to conquer.
We may be quick to judge Habakkuk but we must all admit that we probably have the same type of complaint with God sometimes. We want God to do things and He does but when He does them His way we complain because it is not what we expected. Growth in our faith allows us to not only trust God to do things but also to trust that His methods are best.
"You have made men like fish in the sea, like sea creatures that have no ruler. The wicked foe pulls all of them up with hooks, he catches them in his net, he gathers them up in his dragnet; and so he rejoices and is glad." NIV translation
The prophet continues to question God's choice of instrument and wonders why both the good and the bad are to all be conquered. We may ask ourselves why we are subjected to the bad effects of those around us who do not try to follow Jesus Christ. Why do we, as Christians, have to live in this world today with all of its ungodliness? That is similar to the question that Habakkuk is asking God in this passage.