Dear S:
Though your child is only six, she is asking some of the same questions that many adults too are asking about God and the events of and since September 11th. In fact, though I am responding to your question about your daughter, much of what I have to suggest could apply to adults.
To start, every child (like every adult) is different and each must be answered in ways that address their personalities, sensitivities, maturities and understandings. As a father of 4 kids myself, I have seen that each of my children reacted differently to the recent events and each had different questions. You obviously know your child better than anyone, so you will need to adapt what follows to best serve you and your child's needs.
Before getting specifically to your question about God, I'll quote two professionals, Dr. Robin Goodman and therapist Kim Fendrick who offer some general suggestions about coping with the trauma we have experienced. They both encourage helping kids to express what is on their minds (when the child is ready,) and not dismissing their fears. Their thoughts and emotions can be expressed in words, music and art...just like adults I might add.
Dr. Goodman also says "Contrary to parents' fears, talking about violent acts will not increase a child's fear. Having children keep scared feelings to themselves is more damaging than open discussion...But adults must be mindful of stating their opinions as fact or absolutes." Her last point leads me to your question about God. When my children ask me about God I usually start with "nobody knows the answers for sure including me." I also ask them what they think. Their age and maturity then dictates how complex of an answer I try to give.
However, in all cases, I agree with the advice of Rabbi Earl Grollman who says "Fairy tales and half-truths are not proper explanations for the mystery of death...Unhealthy explanations can create fear, doubt, and guilt, and encourage flights of fancy that are far more bizarre than reality."
So what is the truth and how do we explain it to kids? Personally, I resonate with much of the thinking of Rabbi Harold Kushner. I suggest you look at his book "When Children Ask About God." I can't do justice to the book in a sentence or two, but in summary, he suggests that God has created the laws of nature (gravity, night and day, life and death etc.) that give us a general order to our lives. After that, God does not directly intervene in our lives other than giving us abilities to do God like acts like finding strength when we are weak and comforting and healing ourselves and others.
As he says, "The most useful question....is not 'Why did it happen?' but, 'Now that it has happened, what can we do about it.'" This is a question we can and must now answer, together with our children and other adults.
You may not agree with Rabbi Kushner's theology so your own will influence how you care to answer, but as you wrote, you are not sure yourself. You are not alone...as noted in the subtitle to Kushner's book "A guide for Parents Who Don't Always Have All the Answers." Of course, none of us have all the answers so we need each others help.. especially now. If others have suggestions they'd like to send in, I'll pass them on. I'll end with a reference to a website with many helpful resources for readers whether they have kids or not: http://www.jewznewz.com/for_parents.phtml .
Love to your daughter,
Gil