Flags aren't for rule breaking, they just mean enough people found your comment inflammatory or otherwise objectionable enough to hit the "flag" button.
If you have a link to the flagged comment, I can probably help you understand why HN users would have flagged it. This comment is getting downvotes because complaining about downvotes and flags always does.
It doesn’t show as flagged for me. Time heals all wounds, if your comment is not objectionable it will usually be vouched for eventually. Which is one of the reasons it’s a rule here that you don’t complain about voting. Such comments also rarely age like wine :)
You can complain, you'll just get a small karma hit for it. It's inevitable because it's off topic, but karma on HN is more or less meaningless anyway.
If you have a link to the flagged comment, I can probably help you understand why HN users would have flagged it. This comment is getting downvotes because complaining about downvotes and flags always does.