Just flying I had no trouble. They did put a red tag that said BSO on the bags - whatever that means. I flew into Albany, NY with rifles with no trouble. The worst thing that happened to me was I came back from Pennsylvania to San Antonio and the gun case did not make it! I immediately told the bag complaint person that I wanted the law to come over as I wanted to report a theft of several firearms. That caused some excitement. The next day, the gun case was delivered (with contents to the house). I was told the reason it didn't make it was that the plane was overweight so they decided to put dangerous cargo in another plane (so that one could blow up?). What? I never got more info.
One one flight, the gun case was put in the bag office and I was paged. They told me they want to avoid a claim turntable theft. Forgot where. There was a guy in back of me on this flight who checked a big rifle case with no problem.
Not a gun but years ago, I had a copy of Gary Kleck's book Point Blank in my carry on. The TSA person - saw it was about guns and said: Lordy, he will kill us all! So I said - it's about gun control and she calmed down. That ranked with the agent who flipped out over my automatic lead pencil which had a wire in it to put the lead in place. A National Guard captain in full gear had to save my pencil from her (this was Nov. 1911). This flight - the pencil, a steel pen, a Surefire and 5.11 flashlights made it through - but my steel capped shoes buzzed on me and my laptap got swabbed down.