Avoiding dark alleys is certainly normal advice in Japan as well. http://pds.exblog.jp/pds/1/201112/13/73/b0015373_19495370.jp...
While it is officially advised, as many things in japan are, they are by no means mandatory. In japan you might just as well see a sign saying "don't go out in the rain, it's dangerous".
in japan, i've been to plenty of dark alleys during night time, visibly carrying cameras etc. and i've yet to be encounter anything bad. i think it is fairly safe to say, that japan is a LOT saver than most parts of the world.
Not really a defensive reply, because I don't live in the US, but across the border in Canada we have a very similar culture and very safe public transportation. I grew up in downtown-ish Toronto and never saw a crime. There are crimes, just not too many that people fear taking public transportation. A typical subway ride in Toronto has plenty of people in suits. Bus transport in other cities in Ontario is also quite safe.
We've put up with crime for so long in the USA we've forgotten places actually exist without most of it. We've gotten so used to it we think it's normal to "avoid dark alleys" to "pull out your car stereo and don't leave anything visible, even a jacket or risk getting your car broken into" to "don't go to those parts of town"
None of those apply to certain countries.
now watch the defensive replies :(