Although I agree with this point, I wonder if the removal of downvotes would alter the usage of 'flag' by a measurable amount, and flag be used by some as a proxy for when they would have used a downvote instead.
I think this is what dang means when he talks about building the technology to make the site YC wants. Users will use the features to get the results they want, often against the intentions of the site creators. reddit and the ongoing battle against 'downvote isn't for disagreement' in every sub is a good example of this. What mods want it used for is different from what users want to use it for, and obviously the users win.
Taking away the downvote button might seem like it would fix the problem, but as you point out, it would probably just shift the site behavior so that people use different features (flagging) to achieve the same result.
My guess is that the downvote system is an intentional encouragement of laziness in order to drown unpopular comments for whatever reason (sometimes valid such as noise, sometimes to intentionally suppress challenging viewpoints) while avoiding the heavy burden of moderation.
Just like Reddit's system, it is heavily flawed and easily gamed, as seen pretty much all the time here.
Having used things like Facebook, however, I don't think a single upvote is a better system; a bad post from somewhere or someone with enough momentum gets enough upvotes to perhaps go viral — even if completely factually incorrect. You need the -1 to balance it out, sometimes.
I don't tend to downvote if I disagree (and I'd argue, I think, that one shouldn't — if you disagree, comment); I typically only downvote if the post is extremely factually incorrect, not adding to the discussion (for example, repeating an earlier point or asking a question that is answered in an ancestor comment — i.e., not reading), or is rude. (I reserve flag for extremely bad posts — and often HN has beaten me to it.)
Not saying a +1/-1 system like Reddit or HN is perfect, nor is it the only alternative to a just-+1 system. One could imagine, for example, giving experts in various topic areas more sway in their vote, if you knew the topic of a given article (they should know what they're talking about); but that could just as easily backfire if a newcomer has a completely valid — if unconventional — idea.
Taking away the downvote button might seem like it would fix the problem, but as you point out, it would probably just shift the site behavior so that people use different features (flagging) to achieve the same result.