I recently read somewhere of someone mentioning a "green flag" as a "good" indicator, which struck me as a little odd; it wasn't until later I realized they were using it to contrast it to "red flag" as a bad indicator. And yet there aren't any situations that I can think of where there are any green flags--we just have red flags to warn of danger. "Green" only comes in the context of traffic lights, which I suspect were well off the mark by the time the phrase was coined.
My original thought was that the opposite should be "checkered flag" as an indicator to "go ahead" (as in auto racing)...but that doesn't really mean the same thing as a "good indicator" nor are red flags actually used in that context, either.
So I looked it up. Turns out we've been raising the red flag for alertness for a long time, almost always in the context of the military and almost always signifying blood. SO, really, there isn't an opposite of that to mean a "go ahead" unless we want to go with "green light," and at that point we're mixing metaphors.
I'm sure there's plenty of other incidences where we can come up with something that has an obvious opposite, and yet really shouldn't given the origin of the phrase. Such are idioms, I suppose.