San Francisco is safer (in terms of violent crime rate) today than it was at any time in the 1990s. (It also went up from the late 1990s to the mid-00s, so if you only started feeling safe in the late 1990s, that was probably your personal circumstances, not the actual safety of the city.)
Fair enough. I don't think it's that unsafe now either. It just felt like it had a lot more rough edges when I was younger, but that could've been due to differences in experiences as I got older.
