It's human instinct, especially in males to subconciously give ourselves a "ranking system" where each of us knows our position in any given group. It's also instinct to want to be as high up the ladder as we can get, because as the old saying goes "shit always goes down".
In the general social ladder, nerds/geeks/more than casual gamers/warhammer fans/anime fans are pretty low down in general. So much so that the higher ups won't notice any difference. Just as we don't see any difference in the atheletes/the naturally good looking/the people born into well off families/popular people who shall now be known as League 1. League 2 (nerds etc) generally view all of league 1 to be assholes for some reason or another. Within both Leagues, all different sub groups or individuals want to get to the top, or finish higher than others.
So we then get, as you put it, nerd on nerd hate. Individuals from league 2 rally behind their chosen group, be it anime, dnd or whatever, and start chest beating, trying to show themselves as "better" than the others. Some may be part of multiple sub groups, at which point they will generally bash what they are not a part of.
Of course it's not entirely as simple as I've just explained it, but if you remember that deep down we are all still animals things become easier to understand.
As an aside, although it should help explain my point. Next time you go out and see a group a girls, notice that most of them will generally be of a similar level of attractiveness. One, or possibly two depending on the size of the group will be far less attractive, most likely overweight aswell. Now conciously they are all friends and it's all good, subconciously, the main group of girls hang around with the less attractive one because it makes them look more appealing.
Now watch the way they move as a group. The most confident/best looking will always be at the front, the least attractive at the back of the group. I could be entirely wrong, however my friend and I spent an entire night at a club testing this theory and every group of girls that numbered 3 or more had the same thing going on.
I would go into male groups aswell but that's detracting away from the thread even more, so the tl;dr answer is: We're still animals, like it or not. We still think like them and act like them even if we don't realise it, which is why you will always find conflict between different groups of people.