Nazi Protagonist

Although Nazi Germany and individuals affiliated with the Nazi regime are typically cast as villains (and for good reason), there are occasional works of fiction where a Nazi, or a person who is associated with the Nazi-era German government or military, is presented as a protagonist, rather than an adversary for the protagonist. On occasion, the character in question is a true protagonist and not a Villain Protagonist.

Be careful though, not All Germans Are Nazis.

Anime and Manga

 * JoJo's Bizarre Adventure. Rudolf Von Stroheim is not the protagonist, but one of the main good guys.

Comics

 * Master Race, a very famous Bernard Krigstein comic, had this as a twist.

Films -- Live-Action

 * In Downfall, the events are told from the point of view of the Germans during the last days of the Third Reich. Hitler's secretary Traudl Junge, SS medical officer Ernst-Gunther Schenk, and Peter, a young German by inducted into the Hitler Youth to defend Berlin, are the three main protagonists.
 * Schindler's List. Oskar Schindler starts out as one of these. He gets better later on. Much better.
 * Field Marshal Erwin Rommel himself in The Desert Fox.

Literature

 * The police detective in Robert Harris's Fatherland, despite the novel being set in an Alternate History where the Nazis won World War II, isn't a Nazi himself—it's mentioned that his career has suffered because he refuses to join the Party.
 * The Draka series of novels by S.M. Stirling, in which the Nazis are fighting against the eponymous society (which is even worse than the Nazis).
 * Harry Turtledove's Worldwar series depicted an invasion of Earth by space aliens in the middle of World War II. The series focused on the response by the five main human powers (the United States, Great Britain, the USSR, Nazi Germany and Imperial Japan) to this attack. Among the human protagonists were Jaeger, a Wehrmacht tank officer, and Otto Skorzeny. Yes, that Otto Skorzeny.
 * Apt Pupil, by Stephen King. The two main characters are an ex-Nazi and a young boy who wants to learn everything about his time in Germany.