Ever notice how easy it is to find a particular view about the world utterly convincing? How we tend to adapt particular attitudes, some of them passionately and thoroughly, and at times find ourselves alienated from our own potential to understand another's viewpoint? Like finding ourselves at the driving end of an ideological spear, we suddenly realize we are defending a view, exploring how it works itself out in the real world. Take race and gender as an example; you notice how it permeates society, so you begin to (if it has been sufficiently imprinted on you by the university, or a particular interest of yours), see how it all plays out. You play the conquistador of equal rights, the bringer of multiculturalism. Seeing a real problem, a part of you sympathizes with the efforts, and wishes to play a part in the on-going war "against" ignorance, injustice and inequality.
Or, in the case of the new atheists, part of you actively takes on a personal effort to immerse yourself in rationalist thought, watching dialogues between the greater ideological spokespeople, reading books and joining forums. You identify with the cause. Your forum tag becomes Dawkins quotes or Sam Harris, or any particular rationalist for that matter. Your identity, at this point, has immersed and linked itself entirely, or at least strongly with the movement, the effort, and the ideas involved.
In both of these cases, we allow ourselves to be strongly shaped by our passionate interest for a subject that we agree on. It seems natural for humans to bind together and identify with groups, be they larger or smaller. Yet it also seems at least a little dangerous in that by giving our minds over to be, in a sense, conditioned by an ideology (fanatic or not) is to limit our ability to understand another. By building the mind for specific tasks, we allow it to be less open to the receptivity of others (Not always, but frequently).
I find in many of the debates online, no matter what particular argument is going on, both sides fail to make the jump to a common ground in which one begins to thoroughly understand the other. Mistakes in interpretation, or simple strong identification with a viewpoint clouds the debaters judgement so that he or she may often miss a critical and interesting point about the "opponent." On the same token, the debater may even make poor arguments based on not thoroughly seeing what the oppositional view is. The fact that we disagree, conceptually, is not something that can be avoided. It goes almost without saying that to disagree is almost natural for us, but the inability to perceive another's attitude, to see through their perspective is something that is so far and few between, yet so important as the information age progresses. Unless we really do wish to see fragmentation, it's important for us to accept that perhaps we cannot entirely understand another's view, but maybe that is not necessarily important. Even agreeing or disagreeing, it may seem, may not be terribly important - save some vital issues and decisions.
In fact, that's the main point trying to be made here: Our agreements or disagreements, our theories and attitudes and ideologies we often follow are more about identification, emotional attachment and willing self-conditioning rather than objective "arguments" or clearly grounded perspectives.
Our ideas are ingrained into our psyche. They are rooted in our conscious and our unconscious, our battlefield, or playground of concepts in which we identify, and this occurs through various environmental and internal factors. The more we understand it's less about "I disagree!" and more about, "I identify strongly with this concept, and since this is who I am, I must defend myself!" We essentially allow our conceptual mind and emotional unconscious to continually shape our identity through time.
Perhaps more often than not debate is little more than ego battling ego, identity versus identity, using the other's defeat to build up your own. In many cases, our interests are sincere. They are not outright selfish, but to observe how we identify with a particular cause, it would greatly help us to not be so blinded by our own belief systems, and so arrogant with others.