My underlying theme on my commute is: there are good people in bad neighborhoods and bad people in good neighborhoods. No place is 100% bad or good.
I commute through a neighborhood that is questionable. Perhaps not the toughest area of town, but it comes a close second. I ride through at 5:30AM and again on the way home.
To be honest, I've had *way* fewer issues in the bad neighborhood during my commute than the "good" area. In the "bad" area, at the time I go through, people are going to/coming from work. When they see a bike, they give me room. In the "good" area, cars come too close and turn in front of me. Many days I prefer the "bad" neighborhood.
Don't get me wrong, I have had issues in the rouger end of town. A couple of late teen/twenty somethings thought it would be fun to try to scare the biker; there was the morning with the guy in the middle of the road; etc. But, overall, I rarely feel uncomfortable. And, you know, in the "bad" neighborhood, there are actually people out on bus corners, so you are never really alone.
Now, if I were going through at 10PM, I'd probably feel differently, but during commute time....you're just another commuter. And, there are other neighborhoods I wouldn't go through at noon. Each is different. You need to consider your city and evaluate.
2009 Waterford RS-14 S&S Couplers - Brooks B68-Anatomica - Traveller
2008 Waterford RS-33 - Brooks B68-Anatomica - Go Fast
2012 Waterford Commuter - Brooks B68-Anatomica - 3.5-Season/Commuter
2011 Surly Troll - Brooks B68 Imperial - Snow Beast