We can read this quote as relating primarily to Gene's relationship to Finny in A Separate Peace. This relationship is central to the story of the novel and is also at the root of the novel's themes of change/growth, innocence and the loss of innocence, and loyalty. 

The love mentioned in the quotation should be read both as a general comment on important relationships and also in specific reference to the bond of friendship shared by Gene and Finny. The two are profoundly connected. They are best friends. Yet, the relationship sours when Gene suspects that Finny is competing with him and trying to keep him from doing well in his studies. 

The friendship and love that is shared between the two of them is lost when Finny falls from the tree. To some extent, the love is revived, but in the end Finny dies and any possibility of a full repair for the relationship is lost. 

The violence mentioned in the quotation should probably be read in reference to Finny falling from the tree andhis fall down the stairs at the end of the novel. One fall, of course, leads to the other and so we can say that each of these violent falls is responsible for Finny's death. 

The quote becomes somewhat ironic when we see that the love Gene felt for Finny and the pain, guilt and regret he feels for Finny's death are actually lasting for him. Years after the events he returns to the school to purge himself of these memories, which are very real to him and lasting. 

However, there is no sign of the events on the school grounds. The history between Finny and Gene that is recounted in A Separate Peace has effectively been erased by time. The tree no longer stands out to anyone but Gene. 

Explain what is meant by this phrase from the novel A Separate Peace: "Nothing endures, not a tree, not love, not even a death by violence."

This quote appears in chapter 1, right before Gene begins telling the events that occurred at the school. Prior to the quote, Gene is wandering over the grounds at Devon school. He mentally makes comments about how things look the same, yet different. He recognizes all of the places and things that he is looking at, but they all look smaller and less imposing than they once did. This is especially true once Gene finds the tree that plays such a central role throughout the rest of the story:

This was the tree, and it seemed to me standing there to resemble those men, the giants of your childhood, whom you encounter years later and find that they are not merely smaller in relation to your growth, but that they are absolutely smaller, shrunken by age.

The quote shows that Gene understands why everything looks different. First, he has gotten bigger. Second, time has passed and he has matured.

So the more things remain the same, the more they change after all—plus c'est la même chose, plus ça change. Nothing endures, not a tree, not love, not even a death by violence.

There is a common phrase about time that says, "Time heals all wounds." It doesn't explain how time does this, but emotional wounds tend to fade as time passes. We mature and learn they aren't as big of a deal as they used to be, or time simply passes and releases us from many of the specific painful parts of the memory. Gene's comment has this sentimentality about it. Time has passed and nature has physically changed the tree, but time has also changed and softened his memories of the tree. His feelings about the tree and his love for his friends from that summer have also not endured in exactly the same way as they used to exist.

Explain what is meant by this phrase from the novel A Separate Peace: "Nothing endures, not a tree, not love, not even a death by violence."

In A Separate Peace," the narrator returns to the scene of the crime, so to speak, years after the events that he relates to the reader in the novel take place.  The statement you ask about refers to the narrator's reaction to those events.

The tree is only a tree, when Gene returns and sees it again.  The associations and mythical-like qualities the tree held for him those years ago are no longer present for him.  The tree is no longer threatening or "bigger than life."  Also, he did not despair over what he did to Finny.  He has learned to live with it.  And his love for Finny was very much envy and jealousy and obsessive suspicion.  Gene's statement is a sophisticated response, in that he doesn't try to explain away what he's done, or try to give some moralistic one-liner to demonstrate some lesson in all this:  he doesn't try to assign some cosmic significance to the events.

Time has passed and nothing lasts.  Life continues.  Gene has moved on, as, of course, we might assume other characters have--except Finny.