I think that the rudeness in religion debates can come from all and any quarters. It isn't that believers are all sweetness and light and atheists are all angry and spiteful, or the other way around. The rudeness is the responsibility of the individual, regardless of what they do or don't believe.
At the same time, we must all try and understand that when we are discussing matters of religion or alternatives to religion, then we are discussing matters of profound and fundamental personal importance to those concerned, on both sides of the debate. Feelings can run very high. All the more reason in my view, to tread carefully and be polite. On the other hand no one should feel so intimidated by the possibility of causing offense as to allow themselves to be oppressed in the proper expression of their thought. We have worked long and hard for freedom of speech and should value it highly.
I'm an Atheist and have a strong interest in evolutionary biology. This view leads me to acknowledge my kinship with all life on the planet. So I see everyone as being quite literally, my relatives; my brothers and sisters on the tree of life, so to speak. In that regard I have a responsibility of respect towards all living things, my religious sisters and brothers no less than others. I am always at pains to point out that I argue with ideas, not with the people that hold them.
Unfortunately, in the same way that a very few (but very vociferous) Atheists prejudge all religious people as inherently stupid and dangerous, so there are quite a number of religious people who enter the debate with the preformed assumption that the non-religious person is an agent of Satan and cannot be trusted. Clearly, when these two meet, it bodes ill for any kind of intelligent conversation to ensue!
However, I do think, given the huge impact that religious belief of any kind has on all our lives, it cannot be set apart as somehow above debate. It is of course, inherently difficult to engage in a rational debate with someone who believes their ideas, however lacking in evidence or originality, are of Divine origin and above all criticism from the outset. I think a lot of Atheists find that very arrogant and frustrating, as you might imagine. Equally, an Atheist who has adopted non-belief as a dogma (which is an oddly irrational thing to do) is wearing pretty much the same colors.
It is not an easy business, whichever way you look at it.