If you want something comfortable to wear to work just wear normal shoes if the ride is short. Otherwise bring something to change into.

All the half ankle and low cut boots don't seem to offer more protection than normal footwear. They may have some more padding but I can't see that saving your foot/leg in a serious fall where you wish you were wearing protection.

If you are going to only have one pair of boots make them full length ones. Keeps you feet dry when its wet (to a limited degree), keeps the wind from pounding your shins on long rides, and in the even that you do crash, it'll save you some broken bones and tissue damage.