Why debate questions of religion?

Recently, I took part in a discussion with a friend that touched on issues about which I care very deeply. The rationality of religious belief; the wisdom of religious belief; the nature of knowledge itself--what does it mean to be certain?

Although we did not tread any ground that hasn't been covered before by people with far more pedigree and knowledge, I thought it was a healthy, it somewhat heated, discussion on these "Big Questions" between my nonreligious self and my considerably more religious friend. I was surprised, then, when a third-party posted the following:

"If you are a Atheist. . .Why do you have to challenge GOD????? This is something you chose not to BELIEVE IN. . .Why would you have to have this arguement with members of the Christian Community????? Do you try to challenge a belivers faith in thier GOD just to prove 'your point'? Who appointed you chief antagonist?????

I think you are looking for something in your life that you do not 
have. . .A sense of belonging in a Christian Community. Ah! First you would have to BELIEVE Iin the generousity of GOD."

These words ring with the sound of a defensive anger, somewhere between "how dare you?" and "why can't you just live and let live?" And to a certain extent, I understand. We all have our sacred cows, so to speak, and it can be a deeply affecting, negative experience to have them bluntly criticized by outsiders. And religion is usually the most sacred cow of all.

But while I understand some of this anger, I also believe that it's misplaced. In fact, I think the author of the above comment misunderstands the purpose of the debate in question, and maybe even all similar critical responses to religion from the atheist community. So I feel an obligation to answer, from my point of view, the questions posed.