They can usually mean the same thing. For the most part, "are" is a present term, and "did" is a past term.
So "Are we finished?" , can refer to at the moment asking someone if you are finished.
"Did we finish?" , can refer to something in the past. It can be a minute ago or days ago. Keep in mind so long as the time is in the past.
While eating dinner at a wedding you look to your cousin as you notice the plates being taken away and asked, " are we finished? "
Three days ago you completed a task given to you by your professor. You worked on it with a fellow classmate. You seem to have forgotten if you finished it so you ask them, " did we finish the assignment? "