I was trained to respond to peer review of my submitted manuscripts as straight up as possible. By this I mean I was trained (and have further evolved in training postdocs) to take every comment as legitimate and meaningful while trying to avoid the natural tendency to view it as the work of an illegitimate hater. This does not mean one accepts every demand for a change or alters one's interpretation in preference for that of a reviewer. It just means you take it seriously.
If the comment seems stupid (the answer is RIGHT THERE), you use this to see where you could restate the point again, reword your sentences or otherwise help out. If the interpretation is counter to yours, see where you can acknowledge the caveat. If the methods are unclear to the reviewer, modify your description to assist.
I may not always reach some sort of rebuttal Zen state of oneness with the reviewers. That I can admit. But this approach guides my response to manuscript review. It is unclear that it guides everyone's behavior and there are some folks that like to do a lot of rebuttal and relatively less responding. Maybe this works, maybe it doesn't but I want to address one particular type of response to review that pops up now and again.
It is the provision of an extensive / awesome response to some peer review point that may have been phrased as a question, without incorporating it into the revised manuscript. I've even seen this suboptimal approach extend to one or more paragraphs of (cited!) response language.
Hey, great! You answered my question. But here's the thing. Other people are going to have the same question* when they read your paper. It was not an idle question for my own personal knowledge. I made a peer review comment or asked a peer review question because I thought this information should be in the eventual published paper.
So put that answer in there somewhere!
*As I have probably said repeatedly on this blog, it is best to try to treat each of the three reviewers of your paper (or grant) as 33.3% of all possible readers or reviewers. Instead of mentally dismissing them as that weird outlier crackpot**.
**this is a conclusion for which you have minimal direct evidence.