Note that this is separate from the flares themselves, which are also not allowed.
Probably because too many people have accidentally packed loaded flare guns on the plane. A loaded gun is only dangerous if someone uses it. A flare gun probably doesn't have much in terms of safeties so it has a better chance of going off and starting a fire. A single bullet isn't going to do nearly as much damage if the gun somehow went off on its own.
You have to show the check in counter that the gun has no bullets in it. So I don’t understand how you could accidentally pack a loaded one.
"Mistakes were made" :/
TSA got upset their low level employees couldn't be subsidized by stealing from bags with flare guns checked in them (which were the easiest to obtain compared to a gun)