A few suggestions:
1. Don't stop in sketchy areas. (I know, duh.)
2. Lock your bike when you can't see it.
3. Lock your bike at work in such a way that it won't fall over.
4. Uglify that sucker. A few stickers, maybe some duct tape, wrap strips off an old inner tube and tape it together with some colored electrical tape, etc. Make the casual observer ask, "Why would I want that bike?"
Then ride it and enjoy it. If you've taken reasonable precautions, remember it's a relatively inexpensive bike you bought for pleasure as well as utility.