I have had an ops agent threaten to check my tiny cooler bag one time because I wasn't in uniform. I politely explained that I was a commuting crew member, but he wasn't hearing it. I asked him to show me the regulation that he was talking about and he relented under frustration.

I looked it up later, and sure enough, it is a thing. When you aren't wearing a pilot uniform, you fall under TSA rules for peasants.

That was one commute out of many, so I don't think it's pervasive, but it exists. Worst case scenario, they will check one of your bags.