An unshod horse can do that kind of damage. I was stepped on back in 2009, and yes, I was wearing boots. My mare was unshod and stepped back onto my foot. When I screamed, she sat back and pivoted and got off of me. My foot and leg swelled to HUGE proportions and my boot had to be cut off. Because of my boot, she didn't cut the skin, but because it was such a severe crush injury, I ended up with compartment syndrome in my left foot and leg and almost lost my foot. I wasn't able to bear any weight or put on a shoe for over 6 months and it was almost a year before I could stand even a lace up boot on that foot.
I have had multiple surgeries since then, and have permanent swelling in that foot and can no longer wear certain kinds of shoes because I can't get in past the swelling in my foot. I have pretty much constant pain in my foot, I lost motion and feeling in 3 toes. I can still ride, but I can't stand or walk for long periods without my foot hurting A LOT.
So, moral of the story, wear your boots but more important pay attention to where your feet and your horse's feet are because even with a heavy leather boot on you can still end up with severe damage.