The problem that HN faces is that because of the voting system those drive-by valueless negative comments are getting amplified all out of scale relative to their value.
Imagine being in a restaurant. It's not so bad if there is someone in the far corner having an argument that you can just barely overhear or something a few tables over having a cell phone conversation. However, if the volume of those conversations were amplified such that you could barely continue conversing with the person across the table from you then it starts to become a very serious issue, and if that became the norm at that restaurant you'd probably stop going there as often.
Some comments are on-topic and are helpful, some are on-topic and humorous. Some are off-topic and also helpful, some are off-topic and worthless. As so on, and so on.
With only one direction we can "push" a comment (and only one direction with which we can view comments, up & down), there is not all that much filtering that can go on.
Sometimes I enjoy reading the "funny" responses. What if this was a separate comment axis that I could view? Others may not be interested in such a thing, and could ignore it.
In any case, the format of HN doesn't lend itself well when people from all over the world bring their own views into a single topic. I don't know if a good way of solving it easily other than being ruthless about removing content that doesn't belong.