https://maps.app.goo.gl/zhZdA5tWGAKunM2e8
(This is widely considered a misfeature of San Jose - it limits the height of buildings in downtown San Jose to 10 stories because the downtown is directly under the flight path of arriving flights, it limits runway length and airport expansion, and it means that planes and their noise fly directly over key tourist attractions like the Rose Garden and Convention Center. If we ever had a major plane crash like this one in San Jose it would be a disaster, because the airport is bounded by 101 on the north, 880 on the south, the arriving flight path goes right over downtown, and the departing flight path goes right over Levi's Stadium, Great America, and several office buildings.)
So while downtown being in the flight path is a risk there was some method to the madness which caused that alignment.
In addition, the terrain rises in both directions (so sharply on one side that planes can't use ILS when landing from that direction).