I find that riding through the "wrong" part of town is not really a problem. Perhaps it's because I dress like a homeless person when I'm on the bike but I find people generally leave me alone. You're on a bike how much could you really have that some thug wants? I've riden through the worst parts of Boston, MA; Buffalo, NY; and Washington DC and never had a problem. You may also find that the more you ride through the less likely you are to have a problem. In my experience once you become part of the scenery it's almost like the "bad people" accept that you're going to be there.