I have the same fears, although I am not worried about thugs. My biggest fear is of things I cannot see. There are cracks and holes in the road. There are curbs that even though i've done the route a hundred times before, I might forget. Then there's road debris.

This is what i do:
if it's dark, it can't be too cold or too wet.
so I will ride in dark but not cold and dark
or cold and WET and dark.
If it's raining and dark, i will not ride. If it's just a tiny sprinkle, i might.

It helps a lot that my husband has literally LEAD me to work "see, this isn't so bad" but even though, I haven't ridden to work in almost a month now.
come February, when the days are getting a tiny bit longer, I will start wanting to ride to work again.

of course, I am worried about cars too, but that's true no matter when I ride, and I too am lit up like a christmas tree.