Forget About It, Jake…
Watching this movie for the first time, you might think, "Why is this called Chinatown if so few of the scenes are actually set in Chinatown?"
The key to this is in the (awesome) dialogue, which discusses the fact that Jake used to work in Chinatown. And when we finally do arrive at the actual Chinatown, it's for the movie's final scene.
Jake tells Evelyn that when he worked in Chinatown he tried to do "as little as possible." This is because he had an experience there that shook him to the core:
GITTES: I thought I was keeping someone from being hurt and actually I ended up making sure she was hurt.
Faced with a culture he couldn't navigate and didn't understand, Jake decided that inaction was the safer path. For him, "Chinatown" refers to a realm of bewilderment and confusion. It's not just a geographical location. It's also a state of affairs in which it's impossible to comprehend what's going on.
Take these lines for example:
CROSS: You may think you know what you're dealing with—but believe me, you don't...
GITTES: [That]'s what the District Attorney used to tell me in Chinatown.
It's an ominous warning that Jake fails to recognize.
In Chinatown, Jake couldn't figure out what was going on. And now, in the current case, he can't fathom that a kindly looking old man like Noah's capable of breathtaking evil. The mini-culture of depravity which Noah has created in his own family remains outside Jake's comprehension until the end—he doesn't discover the truth about the incest (or that Noah's the true murderer) until it's effectively too late.
He's out of his depth, just like he was in Chinatown.
When Jake's assistant says to him at the end, after Evelyn's died and Noah's recaptured his daughter/granddaughter, "Forget about it, Jake—it's Chinatown," he's telling Jake that this situation isn't worth trying to understand. It was always bewildering and screwed up beyond the capacities of even a very intelligent detective.