Comments are appropriate in JSON which is written by humans. If it's written by a machine, of course comments are irrelevant. Situations where you need to automatically make changes to JSON which is primarily maintained by humans are a bit of a special case that I don't think is worth optimizing for; if you feel putting comments in object fields is a better choice in this situation, you can still do that even if comments are supported.

Supporting comments makes JSON more convenient to use in more situations, and it doesn't prevent you from doing anything you can do now.