I think this stems from the separation of ideas from the self, which is really the first step on the road to rationality. Anyone who hasn't made that step feels like they are being personally attacked, and it isn't an easy step to make.

Even if you've made the step in general, it doesn't help when people use status-signaling language in their comments. e.g. "Have you thought of X?" is a lot better than, say, "Clearly you haven't paid any attention to X", if your goal is to actually improve discussion, rather than to get a charge from demolishing your opponent. (I suspect that the concept of a martial art of rationality doesn't help with this, from a priming perspective.)

Setting a frame of etiquette that indicates we are all here to help people become rationalists rather than to show off our own skills at rationalism might help with this.