The fact that the top comment on HN posts is so often some sort of complaint or snarky remark is arguably a problem with HN itself. It's much broader than this post. It's the comment thread of analogue of the tendency of indignation-inducing stories to rise to the top of the frontpage.
Lame complaints may be a problem, but I'm not so sure about complaints in general.
A link like this exists to give you a one-sided case for using an app. Following that up with a counterpoint seems like the most informative way to proceed. I think the HN standard should be that comments of the form "This would likely improve your product" deserve to be voted up, while "Here's why this won't work" should be voted down.
