How does Superman feel about Jason Todd?

What does the graffiti "Joke's on You Batman" mean?

tl; dr: It's a late Robins suit; The assumption is that Joker killed Robin at some point in the past and has haunted Bruce since then.

The film doesn't explain the graffiti. It is supposed to be part of a not yet told Batman backstory. It is possible that part of the story will be told in future films, possibly in a Batman solo film.

However, we can pretty well guess what is going on based on what we see in this movie.

For starters, we know Batman before Dawn of Justice was a vigilante group in Gotham for some time, long enough to become a "legend". We also know he quit this job for unspoken reasons and became bitter and depressed. It is only when Superman arrives that Batman decides to fight crime again.

When we look at the suit:

You can see a stylized "R". This was a Robin suit, but we never see Robin in the film. The strong implication here is that Joker murdered Robin, then destroyed the suit and left Batman to find him. It was the death of Robin that turned Batman into the dark, violent, cynical version of Batman that we see for most of the film.

Bruce makes a number of comments during the film that support this idea, although the name "Robin" is never used and neither is any of the names of Robin characters such as "Jason Todd" (the most likely Robin for it), "Dick Greyson" or "Tim Drake".

Later in the Suicide squad Some of it is confirmed: The introductory graphic for Harley Quinn claims she was arrested and accused of being an "accomplice in the murder of Robin". Knowing that headquarters was closely linked to Joker until her arrest, this again implies that Joker was ultimately responsible.