What's the difference between judging God and questioning God? In my answer to Can man judge whether God is fair?, I gave an example of the prophet Habakkuk questioning God in a judgmental way. God dealt with Habakkuk patiently, answering his questions.

On the other hand, as that question points out, there are people who judge God by deciding He is not fair that therefore should not be worshipped or trusted.

How do you draw the line between judging and questioning God?  Is it ok to question God, but not to judge Him?
Yes. In questioning God, we are admitting that his knowledge and wisdom is superior to ours:

“Why are you doing this?”
“This doesn’t make sense to me.”
“When will you rescue me from this situation?”

Whereas to judge him would be to assume that our knowledge and wisdom is superior:

“You are wrong to do this.”
“You’ve forgotten about ....”

It's a very thin line, but there is a line.