Arlington House, The Robert E. Lee Memorial, also known as the Custis-Lee Mansion and located in present-day Arlington National Cemetery, is maintained by the National Park Service as a memorial to Lee.
The history of that cemetery wasn't exactly started as a memorial to Lee. In fact, it was started to make sure he wouldn't return to live there. I'm glad the house is now kept and funded. It's a part of history, and I'm not of the opinion that we should wipe the slate of all historical references. And I'll go one step more and say that it's a beautiful house.
The United States Army, and the United States Navy, and the United States Government, do choose to honor him, along with of lots of other Confederates.