Comment by Retric
There’s roughly a mile of roads, green spaces, and river between the airport and downtown San Jose which an absolutely identical accident would impact. It’s not very wide, but pilots aren’t going to aim for buildings if they can help it.
So while downtown being in the flight path is a risk there was some method to the madness which caused that alignment.
San Diego's airport, on the other hand, has the a bustling restaurant district, an interstate with frequent bumper-to-bumper traffic, and a dense residential neighborhood all within a mile off one end of the runway -- and a popular shopping area, an elementary school, and a high school within just over a mile from the other end.
In addition, the terrain rises in both directions (so sharply on one side that planes can't use ILS when landing from that direction).