Well, before justifying the most-used title, please realize that this story is often given other titles as well: "The Girl on the Train" and "The Eyes Have It." In short, the title refers to the fact that the two main characters, the girl and the man, are blind.
Well, it often happens that people with good eyesight fail to see what is right in front of them. They have too much to take in, I suppose. Whereas people who cannot see (or see very little) have to take in only the essentials, whatever registers most tellingly with their remaining senses.
We learn at the beginning of the story that the man waiting in the train compartment is blind. Truly his "eyes are not here" in that he can only distinguish between light and darkness. The first sign that the girl shares his blindness is the concern of her parents when they put her on the train. They tell her where to put her luggage and how to act.
The next sign the girl is blind is that she is startled when the man begins a conversation. The girl obviously thought she was alone in the train compartment. The two eventually talk with general conversation about where they are going before the girl reaches her stop. Before she exits, the man tells her she has an "interesting" face, which the girl loves because she is usually told she is simply "pretty."
The true realization of the story comes when the next passenger enters and apologizes for not being as attractive as the previous one. Due to his blindness, the man asks if the girl had long or short hair. The new passenger didn't notice because he was entranced only with her eyes: the things that were of no use to her because she was blind.
So, truly, the passenger "with good eyesight fail[s] to see what is right in front of [him]." The title of the story shows that the eyes of the girl and the man "are not here" because both are blind. The irony is that people who can see are "blind" as well.