I think you're on the right track. In my experience, funny is not downvoted for funny's sake. However, there's a strong correlation between funny comments and short/low quality/insubstantial comments, and the latter will get downvoted.
If you want to be funny, be interesting at the same time. If you can't, then save the joke for reddit.
I think there's a bias against funny and amusing comments, and I think it's appropriate. The internet is an inexhaustible source of mildly amusing, even fairly funny stuff. There's a limited amount of room on the HN front page, and it shouldn't be wasted on humor of the quality that can be found in vast quantities all over the internet.
I certainly don't think there is anything wrong with having a forum where every line doesn't play to the peanut gallery.