It was declined without any comments and I was wondering why. Was it considered somewhat funny and therefore worthy of being left there? Or did I misunderstand the point of the not constructive flag?
I declined the flag.
If you're expecting an answer along the lines of "themz the rulez, and that's it," you're not going to find one here. Usage of comments has always been about shades of gray, because their true purpose is to keep stuff out of questions and answers that shouldn't be there.
If you write a comment that waxes philosophic about the sun gods on a question that has nothing to do with sun gods, and you're only succeeding in causing a distraction and irritating other community members, then your comment is probably going to get deleted as noise, and that decision is not going to get overridden on appeal, because comments are second-class citizens anyway.
If your comment flag is declined because the comment is really not causing any harm, and in fact illustrates in some humorous way that the question might possibly be slightly misguided and that the curmudgeons that frequent Stack Overflow are still humans after all, well, them's the breaks I guess.