I fly with a firearm often. I have never had a problem in fact the check in process is easier and it even saved me some $$. My luggage was overweight and the agent said "it's probably your firearm" and didn't charge me the overweight fee!
Just follow the rules and you're good to go. Also always check both the airlines as well as the airport's rules and regs regarding flying with a firearm.
SIG 1911 .45 ACP
SIG P229R 9mm
Beretta BU9 Nano 9mm
Beretta 84FS .380 ACP
Ruger MKIII 22/45 Target .22LR
PWS (Primary Weapons Systems) MK114 5.56