Force Protection for flying in uniform generally only applies to overseas. Look at it this way - if a whacko terrorist hijacks a plane full of Americans in the US he will accomplish his goals, who cares if there was one dude in the military on the flight? Overseas is another story, because you may be the only American on the flight - and you just clearly identified yourself as a member of the military, so it makes you more of a target.
With that being said, I only flew in uniform if I was going TAD and wanted my carry-on to be filled with something else. That guaranteed my uniform arrived. If I had room in my carry on, my uniform went in there. When going on TAD and had plenty of time before check in (or at MAWTS-1 where check-in happens in civvies), then I'd check my uniform. If my family wanted me to be in my uniform when they arrived at the airport to pick me up, I'd carry it on and change in the bathroom before leaving the secure area. More comfortable that way.
I agree about chatting up the FA's about being in the military. On a flight from Atlanta to San Diego (for SERE school), the FA's gave us (there were 5 of us) more meals, didn't cut the alcohol off (as they were cutting other dudes off), and one of them even introduced us to her daughter (who was on the plane). First class was full, and they even apologized that they couldn't bump us up!