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I understand being afraid.
I commute at four in the morning and leave work in the afternoon. I've had people yell at me, beckon me and so on. The nice thing is, on a bike you can just yell "NO!" and haul a$$ outta there.
I never take exactly the same route home or to work. I never leave home or work at the same time each day. Basically, I'm a woman and this is the burden we carry regardless of our method of transportation. Bicycles are no more or less dangerous than just living your life as a woman in today's society.
Learn everything you can about your bicycle.
Have emergency numbers with you.
Public buses often have bike racks (Check with your city) - if you get a flat and can't change it for some reason.
Carry a cell phone always (even a pay as you go phone)
Water
Shoes with a good, stiff sole. Skate shoes, Keen sandals, Close-toed Birkenstocks, Chrome Shoes (made by Chrome bags of SF). *my feet get tired on long commutes or rides if my shoes are too thin. Short rides allow for almost any shoe.*
A messenger bag or backpack, later - a rack and rack bag of your choice.
Moisture wicking base layers. For all seasons.
Good sports bras! - (if you're gifted in this area at all, you don't want your lady bits slamming about!) 
Good underthings
Flat kit
Knowledge of how to change a tire. (I practiced repeatedly on a junk rim at my local cycle-project. I'm still slow at it.
)
Lots of it is just getting out there and doing it. I share your fears, my grandmother was murdered by a terrible person, in the same city I ride in today. Does it do me any good to worry? No. Does it add to my quality of life? No. Does cycling make me happy? Yes. Does it add to my quality of life? Yes.
Anyways, best of luck! I'm sure I've rambled and there is stuff I've forgotten.
Last edited by moderncyclista; 01-03-2012 at 11:08 AM.
"Things look different from the seat of a bike carrying a sleeping bag with a cold beer tucked inside." ~Jim Malusa
2009 Trek 520-Brooks B-17 Special in Antique Brown
2010 Surly Long Haul Trucker-Brooks B-17 Standard in Black
1983 Fuji Espree Single Speed-Brooks B17 British Racing Green