I think you can point to a number of reasons for the intolerance that too often shows up in these boards (and others):
1. People act differently when they feel they're dealing with strangers. Would there be as much road rage if we knew all the other drivers? How about griping at work about someone in "that other department" for screwing things up. It's amazing to me how often this attitude changes when people meet face to face and form a connection, no matter how superficial or tenuous. There really is no substitute for meeting folks in real life, as opposed to "virtually".
2. The Internet conveys a sense of anonymity and face it, most of us simply aren't on our best behaviour when no one's watching. As PC suggested, I act differently when I'm a guest in a friend's house than I do in my own. For whatever reason, ever since boards began, there have been folks who just don't feel the need to be polite, courteous, deferential, etc.
3. As has been mentioned, some folks are awfully passionate about some subjects. Certainly there is a tendency to overreact among all of us when we feel someone else is being deliberately provocative (not in a good way). That said, I'm so tired of a poster starting a thread and the first dozen posts call him/her a troll. Folks, not everyone spends all day at EnWorld and knows that a particular subject (e.g., 4E) has been debated to death. Give them a break. If it's a real troll, the most brutal response is to completely ignore them and let the thread die of starvation.
4. Who posts matters. It is amazing to me difference in how an opinion is treated solely based on who posts it. Psion can make a statement and immediately have a dozen folks post versions of "ditto". Quasqueton can make the exact same statement and be flamed for his supposed "hatred of 3E". (I mean no offense to either Psion or Quas - they're just the first names that came to mind)
Of course, this is no different than the real world. How many times have you been in a meeting, trying to convince the powers that be, and the person no one likes speaks up...to support your idea.

The kiss of death!
Seriously, there are a few individuals who have regularly crossed the line in being rude, intolerant, ignorant, whatever, that I tune out whatever they say. But I see this happening to too many posters who either don't belong to the right clique, or have a few die-hard haters who seem to enjoy raining on their parade. It gets old fast.
5. We're all opinionated jerks!!!! Ok, just kidding. (Really) But think about it: why post on a board unless you believe you have something important or original or thought-provoking or profound or funny or...to say. We're all a bit like authors, whom Asimov called the most egotistical people in the world because they actually expect people to pay to read what they have to say. I've dramatically reduced the amount I post just by reminding myself that most of what I have to say doesn't add much (if anything) to the conversation. I just wish a few others would follow that example...
And in reference to point 5 above, I hope my post wasn't a complete waste of everyone's time...
