We live in a world that isn't fair. From an early age we learn...
"That's not fair."
"Life's not fair, get over it."
That's usually how the conversation goes. Habakuk was willing and bold to complain. He told God exactly how he felt about unrighteous, ungodly people conquering Israel. In some ways, he was basically telling God, 'you're perfect, but you're wrong for allowing this to happen... how could you?'
I believe God delights in you. God loves to see you moved. Apathy is impossible to work with. But if you're upset or angry about something, there's something to work with because you actually care.
God desires a relationship with you. A major part of any successful relationship is communication. Let God know how you're feeling. Even if it means expressing your displeasure. God delights in hearing your voice and seeing that you really care.