I rode a two wheeler for years and always wore boots. I've owned a Trike for 2 years now and still wear boots just for protection from road debri.
+1, I also don't wear shorts. I've been struck by some pretty good sized rocks and other junk tossed by passing traffic. A few years back I had a dump truck coming the other direction drop a rock which hit me in the knee, the rock was the size of a golf ball. Another strange one was when the tour-pak latch on my dads bike broke and a piece of it bounced off the pavement and hit me below the left eye cutting my cheek. Did I mention I do wear safety glasses because a fairing and windshield isn't total protection.