At the moment this answer has spam flags, but when looking at the link in the answer I don't think that is justified so I added a comment under the answer to that effect and I've seen other people do similar with other flagged answers/questions.
However, with the new flags screen, it is possible for people to flag questions/answers as spam without actually going to the message in question, so the comment won't be seen. I think it might be useful in these instances if there was some way of disagreeing with the flags. Either by making a comment visible on the flags screen in some way or by raising an anti-flag that would show up there. Even if the anti-flag might not actually decrease the flags, it would be useful as an indicator to the people moderating to not just flag without checking first.