I have also put them in a taller suitcase and checked it, when I was going somewhere to ride for a week, and needed to pack the clothes for that long.
But if it’s only for one or two days, I put my boots under the seat in front of me in a boot bag as my other/second carry on item. And I put a duffel bag large enough for my helmet and riding clothes and other clothes, overhead. Those are my two items-- the duffel and the boots. I wouldn’t want to put my boots overhead, I too would worry that someone else’s roller bag would crush them down.
Just a few weeks ago I flew AZ-Iowa-Chicago-AZ to try a horse and did the under-the-seat method. Had no problems through security with my spurs and belt stored down inside my boots.
I’m surprised at all the people saying they wear their tall boots on a plane. I can’t imagine doing that, I hardly ever wear them anywhere outside of riding. My ankles and toes would be bleeding if I wore them that long. An airplane seat is uncomfortable enough already. And anyway in an airport I’d be paranoid about getting jumped or harassed by an emboldened bigot. (But that is probably not a worry for a female).