Is there a metaphorical meaning of Trinity's "You know that road"?

She's being both literal and figurative.

Literally: The road does lead back to the Matrix. They've travelled outside the "Core Network" into an area of the matrix that is sufficiently far away that they can hack into it and generate an Exit. If Neo goes back down the road he'll find himself back in an area with a far greater level of machine control and oversight. Although Neo doesn't know it (yet) Trinity is warning him that that's not where he wants to be if he wants to find out what The Matrix is.

Figuratively: She's warning him that the easy road is the wrong road. He must dare to walk the 'road less travelled' in order to prove himself worthy of joining them in knowing the truth about The Matrix. She's also not-so-subtly reminding him about his recent encounter with the Agents (after refusing to obey Morpheus) and quite how well that worked out for him.

That's actually an old saying. It means being disappointed in how things have been. Doing the same old things in the same old places will just lead to the same old feelings of being dissatisfied with the inevitable and expected results. "You've been down that road before." You already have experience there.

Although a long shot, she might heeding her mentor's advice and passing it on to the newcomer:

From the Reloaded script:

Trinity: You always told me to stay off the freeway.
Morpheus: Yes, that's true.
Trinity: You said it was suicide.

You asked for the significance of roads and this is where it pops up again in the Matrix. One might argue, that the first instance where we hear a reference to "choose the right path" (in the first film) is the instance, where Neo starts following Morpheus' teachings, while not doing so before (remember the office). At the same time, the instance where we again are told about a road Morpheus himself says:

Morpheus: Then let us hope that I was wrong.

And indeed, from this point forward we find more and more that Morpheus himself was misled and Neo has to emancipate himself from his mentor.

Actually she is referring to when Neo did not what he was told to (in the previous scene where he didn't obeyed Morpheus and the agents got him). So the road being showewd in that take actually has nothing to do with the phrase Trinity says.

She's not referring to that specific street they look down when she says "that road." That street is representative of his path through life. Remember, the first word shown on his computer screen while he's asleep at his desk is "searching." (That word fuses that scene with the one before it, when the agents are standing at the spot where Trinity "got out." Agency Smith says, "We're going to need a search running." So they are searching for Neo, and Neo is searching for the truth.) "Searching" is the state his computer is in and it also refers to what Neo has been doing with regard to his life. He knows there is more to life than being a drone in an office and making black market software for money. So when he's in the car in the rain, he's at a cross-"roads" in his life. If he rejects the help and guidance of these people and doesn't take this opportunity to move forward with his search, with his life, he will be back to his life "lived in computers," as Smith says in the interrogation scene.

That rainy, dark, empty street--a street you can't see the end of--is a metaphor for the life in which he will remain if he takes no risks, never goes out of his comfort zone. He will remain in a life of isolation, darkness, emptiness. And having been watching him--watching him follow the white rabbit, ask the question (what is the Matrix?) and go out in the rain to meet them--Trinity understands that Neo is willing to keep searching, that he doesn't want to go back down that road, and that they have to help him and keep him from going back.

Neo has dreamt of that road and fears it. It's also the same road where he fights Agent Smith to the death in Revolutions. But, the Wachowskis admitted they didn't originally intend the Matrix to be a trilogy when they made the first film, but clearly they had plot ideas far beyond the first film. They knew Neo would walk down some road towards his fate, and tied in this scene to his final moments in the trilogy. Brilliant.