My sister-in-law broke her ankle when the bike landed on her foot. In fact, the same thing happened to my cousin when his bike just tipped over onto his foot. Maybe there is nothing that can protect against that other than moving your foot out of the way.
I happen to have broken my ankle in motorcycle riding incidents a total of 3 times now. IMHO, the only way to prevent this is to keep your foot out of the way or have some really major and heavy equipment on your feet.
My first brake was on the race track (turn 3 at Brainerd International Raceway, IIRC) when another rider t-boned me and my bike with his front wheel hitting me in the ankle. At the time I was wearing mid-line standard racing boots like these from Alpinestar:
After that, my wife bought me some "better" boots from Daytona. They have Carbon/Kevlar inserts all around and put your foot and lower leg in a fully contained shell. I'm pretty certain this would have kept my ankle well-enough protected to avoid the break even with the direct hit. The boot would have moved the bike instead of my leg bone providing the force. Here's a picture of Daytona boot's construction:

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However, the Daytona is not comfortable enough for daily riding and all-day wearing. I was out of them ASAP after each race.
When riding dirt, I also want the extra stiffness and protection afforded by a true dirt-bike boot.

But again, not a all-day comfort situation.
I don't wear non-motorcycle boots for street riding but I also don't go to the Daytona or dirt-bike type boots just for the extra protection. I look at my boot decision like I do my decision to not put on leather pants when street riding. True, if geared up, I would be better protected and be less injured during my next crash but it isn't worth the every day discomfort to gain the once-and-a-while benefit.
My personal risk/reward equation accepts the occasional need to grow back skin on my knees and hips. It also accepts the requirement to knit back my leg bones when T-boned. If you read my thread "Just had my FJR1300 knocked out from under me" you will notice the standard street bike boots didn't hold up that time either. But that time, I think I would have had broken bones no matter what. It was the FJR hard bags that saved my foot from being completely pulverized or even detached.
So make your own risk/reward decisions but I will never wear general work boots, always motorcycle boots. If nothing else but for avoiding having laces. That one time 30 years ago when I went to put my foot down and could not--because the lace loop was around my shift lever--was enough to go moto only.
Later,
Kent Larson in Minnesota