As I recall he puts it, it is not fundamentalism itself that is the problem. A fundamentalist Jain (http://en.wikipedia.org/wiki/Jainism) is far less frightening than your average Jain (not that they are frightening in the least either) because the fundamentals of Jainism are extremely pacifist. As a Jain, the more fundamentalist you become the safer you become. The problem then is what the fundamentals of some fundamentalists are.
Also, think about what redthrowaway is saying. He complains that religious fundamentalists "believe that their fundamentalist beliefs must triumph over liberal democracy, and they're willing to blow people up in order to see that happen", yet despite this abhorrence to violence he's quite happy to blow other people up in order to make sure that his beliefs win. Violent religious fundamentalists justify their actions in exactly the same way - you could swap the two sets of beliefs around and this would make perfectly servicable al-Qaeda propaganda!
If I was in favour of bombing every religious fundamentalist, I would be advocating that we nuke the Amish. Clearly, I'm not. Our response to the intrusions of fundamentalism into our lives must be proportionate to the nature and magnitude of that intrusion.
Choice quote from it:
"Unlimited tolerance must lead to the disappearance of tolerance. If we extend unlimited tolerance even to those who are intolerant, if we are not prepared to defend a tolerant society against the onslaught of the intolerant, then the tolerant will be destroyed, and tolerance with them."
It is not a perfect book by any stretch, but I think it covers certain topics particularly well.
There are multiple reasons why they don't come to mind during these conversations though. Perhaps most obviously is that violent fundamentalists without numbers tend to be eradicated fairly quickly, leading to an obvious selection bias that makes us think that violent fundamentalism is something fairly unique to major religions.
I think though the more important cause is that when violent fundamentalists lack numbers there is little to no social pressure to tolerate them. Instead of calling them fundamentalists and making excuses for them, we label them cultists and call a spade a spade.
"rationalize away, and they tend to be quite good at it."
I think there comes a point in time when you have to ask why exactly fundamentalists of Abrahamic religions seem to find it so easy to "explain away" the "peacefulness" of their religions.