I hate to tell you (assuming you've asked similar questions at least once), but others have already had the same question go through their minds - we're not original at all! Finding people in the Bible who've asked similar questions is not difficult at all really. (Check out Psalm 13) But in Exodus 17 and Judges 6 the same question came up. The children of Israel asked Moses, Is God with us or not? It says that they tested God by asking if He was still with them. This was clearly unacceptable to God.
But Gideon asked a similar question in Judges 6 when the angel appeared to him. His response to the angel's statement - "The Lord is with you, mighty man of strength" was not an argument about whether he was a mighty warrior or not - remember he's hiding out at night from the Midianites that he's soon to defeat. His argument was, If God is with us, why has all this happened to us? The angel's response was not one of anger - he simply told Gideon to go in this your strength. This seems to indicate to me that his question was full of strength - but why?
It is my opinion that the two similar questions were rooted in very different attitudes. The Children of Israel were grumbling and complaining and arguing with/about God's presence. They were discontent and probably lazy to boot! Gideon's question seems to be rooted in the fact that he was still looking for God - but felt like He left them. God's different responses in the two similar situations seem to be because of why and how the question was asked. It seems that questioning where God is is okay if we are still looking for Him.
It's all about attitude. Today I will meditate on how present God is even in suffering. Even though my world has changed and I can feel abandoned at times, I'll ask where God went - as I keep my eyes on Who He is. I'll not demand that He makes changes in my life or situation (not that that has ever helped!), but I'll let my soul quietly search for Him and His peace today. Will you join me?