Since I just flew domestically last week... I packed my cue in a 1x1 case in a PVC pipe tightly inside a rectangular shipping box. It protected the cue well.
You will almost certainly have to check the cue. At both ends the ticket agents asked what was in the box, and when told it was a cue the agents said I needed to sign for it. Depending on the size, it could go to the oversize baggage section at the terminal.
I don't have any issues to report, but will admit flying with cues is more hassle than I'm willing to deal with regularly.