Did anyone understand the ending of "Zodiac"?

The evidence acquired by Graysmith that could implicate Allen was merely circumstantial in nature. Circumstantial evidence is insufficient to form an entire case or charges against an individual, as they can lead to one or more conclusions. Without additional physical evidence to corroborate a story provided by the circumstantial evidence, nothing can really be done as guilt can't be reasonably assigned.

Graysmith likely wanted Allen to know he believed he was the killer, but given he already lost his job and wife due to trying to uncover the killer to no avail, it's not very likely anyone would have listened to him at the time.

The intent of the scene is to simply show Graysmith still and will likely always believe Allen was the Zodiac killer, but ultimately leaves everything open for the viewer to interpret. Was Allen really guilty, or was Graysmith being driven insane by his obsession with the case?

Complementing MattD's answer, that scene is also there for another reason. Earlier in the movie, Robert Graysmith (the cartoonist obsessed with finding Zodiac) explains his obsession.

I need to know who he is. I need to stand there, I need to look him in the eye and I need to know that it's him.

This scene is what finally gives him closure.

It is what finally lets him lay off the case, so he can finish his book and close this chapter in his life. After this, he can finally return to his family, and move on with his life.