I saw this article on this site and I wanted to give my Catholic perspective. Here is the link:
http://www.atheistrepublic.com/blog/deandrasek/6-things-religion-can-t-e...

This is an interesting article. I'm a Catholic, and your questions have made me think about my religion. Some I don't know the answer too, so I'll have to look in the catechism or email an apologetic. But I'd like to give my thoughts from the Catholic perspective on some of the questions I think I can provide some sort of "answer" too.

Question 1: Where did God come from?
The universe is filled with "stuff". There are a lot of theories to explain where all this stuff came from- the Big Bang, creation stories from all sorts of religions, etc. However, if we assume that at some point there was nothing, and something happened to make everything, we are saying that something came from nothing. There really isn't any way to avoid this. What made the singularity the the Big Bang originated from? What made God? Either nothing was made into something, or something just always existed, be it a tiny point containing all matter or God. So I don't think that this question can be said to "stump" religions, because I think it really stumps everyone.

Question 2: Why does God care about humans?
Catholics believe that God created humans in his image. A painter loves his paintings, and wouldn't want someone to go and burn them all for no reason. God loves us because he created us, and he loves his creations.

Question 3: Why is suffering allowed?
I don't have a good answer for this one. Catholics have tried to explain it to me, but I always have trouble grasping their answer. Basically, when God made humanity they brought sin into the world (like when Adam and Eve took the fruit from the Tree of the Knowledge of Good and Evil- that is referred to as The Fall of Man), and all suffering and sickness is a byproduct of that sin. God did not intend for humans to ever get sick or experience pain or make wrong choices. I understand this answer isn't really an answer. I mean, Catholics do not believe that a little starving child is starving because of their sins. I'm still trying to figure this one out.

Question 4: What does God get out of giving humans free will?
God gives us free will because he wants us to choose to love and follow him. He doesn't want us to be forced to do it. Forcing someone to love you isn't really love at all. Some people might say that God forces us to follow him because if we don't, he threatens us with hell. However, Catholics don't believe that God threatens us with hell- hell is a punishment for people who do bad things. For example, a judge does not send you to jail- the law you broke does. The judge determines if you broke the law, and if you did, then you should have some sort of punishment. God is just, and so is the universe. If you make bad choices, then you are punished. Another way to think about it is in terms of a parent/child relationship. The child is not forced to be respectful of their parents. They can choose to be disrespectful. However, if they are, they will be put in time-out, which is their punishment.

Question 5: Why make humans eternal?
I've never thought about this before! I guess my best answer is to go back to the painter analogy. A painter loves his paintings, so he wants them to last as long as possible. God loves us, his creations, so he wants us to last as long as possible. He has the power to make us last forever, so he does.

Question 6: Why allow ignorance of yourself?
I've never thought of this one either- my best guess is that it goes back to free will. God gives you the choice to acknowledge or ignore him. He doesn't force you one way or another. The rules of the game are laid out by the Bible and the Catholic Church's interpretation of it, so we know the rules. It is your choice to acknowledge them or ignore them. Catholics also believe that you can get into heaven if you haven't heard of Jesus or God or Catholicism. If you are a good person, you can still get into heaven. If you don't know, then how can you be held accountable? Not everyone knows about Catholicism, but everybody has a moral compass. If they try to do what they truly think is right, they can get into heaven.

I hope some of my answers were as thought provoking as your questions! I think that listening to the perspectives of others is the best way to educate yourself, and these questions have made me think about my religion in ways that I haven't before. I hope my "answers" do the same thing!