Early on, we see that the priest is forced to confess that he is a monkey by being put to "The Question" which is "holy" torture. The victim cannot be released because this would bring into question the authority of the church. Their debate over dinner becomes a metaphor for our current position of forcing confessions through torture, something we clearly understand when it comes to religious matters, but have trouble understanding Nationalism as our modern secular religion.
The French Revolution comes into play, and what's interesting is that the divide between East and West Europe during the Cold War, roughly maps to the areas conquered by Napoleon in the name of the "Declaration of the Rights of Man and the Citizen" which was achieved by bloodshed.
Though Milos Forman has a flair for the historical epic, this is not as amazing as some of his other fair, though there's nothing lacking in any of the content. This seems to be the hit or miss way of the medium of film.
The best part of the film is its "message" about torture, confession, religion, faith, politics, art, and the horrors of war.
"The Spanish Inquisition targets artist Goya's muse." Starring Javier Bardem, Natalie Portman, Stellen Skarsgard, Randy Quaid, Jose Luis Gomez, Michael Lonsdale. Directed Milos Forman. From Esp/USA. 2006. 117 mins.