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 the protagonist, rather than an antagonist. On occasion, the character in question is not a villain protagonist.
Be careful though, not All Germans Are Nazis.
"Master Race", a very famous Bernard Krigstein EC Comics, had , in a Twist Ending, a Nazi war criminal protagonist. Up until that point, you would misidentify him as a Holocaust survivor.
Heinrich Augsberg of Requiem Vampire Knight, who in life was a Nazi soldier who committed many atrocities, but who in the Crapsack World of Resurrection has been reborn as one of the few vampires who still retain some kind of conscience.
The POV character in the two-page Sin City short story "Rats" is an escaped Nazi war criminal who served in an extermination camp. "Rats" is what he called the Jews he murdered there. At the end he is killed by a Nazi Hunter.
The stories in the Uplifted series are primarily told from the point of view of Joachim Hoch, an officer in the Waffen SS, who is assigned to conduct a charm campaign for the stranded Quarians. An ardent nationalist and anti-Semite, his views gradually soften through the course of the series, ultimately falling in love with one of the Quarians. Erwin Rommel could fit the same category in the sequel, where he plays a major role alongside Hoch. Hoch would qualify as a true protagonist, not a villain protagonist. Admittedly the stories take place in the context of an Alternate History where the Quarians decide to uplift humanity in a desperate bid to end the exile.
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 boy inducted into the Hitler Youth to defend Berlin, are the three main protagonists, though Junge was not herself a member of the Nazi Party.
The Night Porter centers around the sadomasochistic, romantic relationship between a former Nazi and a Holocaust survivor. Unlike most of the other examples on this page, he's an unrepentant Nazi, which is awesome.
North Face is the true story of two Bavarians and two Austrians scaling a mountain. All four men are shown to support the Nazi regime, the Austrians looking forward to the Anschluss. Through out the movie, Nazis are shown as just regular people, not expressively good or bad.
All the main characters in Conspiracy are German officials of the Nazi regime.
Kurt Gerstein from Amen is member of the SS, and a former Nazi. He was expelled from the party in 1936, before the events of the film.
In Das Boot the entire crew are members of the kriegsmarine and the protagonist, Werner, is a war correspondent from the german propaganda ministry. Actual pro-nazi feelings amongst the crew are low, however, as the crew of the U-96 consists of the "old guard" of pre-nazi sailors.
The Night Of The Generals is about an Abwehr Major named Grau investigating the murder of a prostitute in German-occupied Warsaw in 1942. The three major suspects turn out to be three German general officers.
The Big Time by Fritz Leiber has a sympathetic Nazi, though in a completely alien context. (It takes place in a background of Time Travel and changed timelines, in a recreation station between dimensions.)
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. He is, however, a member of the SS, albeit a version of the SS that has been transformed into what is pretty much a civilian police force.
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 World War 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.
J Robert Janes's St Cyr and Kohler detective novels, set in World War II France. Hermann Kohler is a policeman in the Third Reich, and hence by default a Nazi. He isn't by any means an ideological enthusiast for Nazism, though, and does his best to protect innocent people from both the idological Nazis and the straightforward crooks and psychos who prosper under the regime.
Watch on the Rhine and the sequels co-written by Tom Kratman features rejuvenated Waffen SS troops brought back from senescence to fight off the Posleen invasion of Germany, as much of the Bundeswehr off fighting on other worlds and what remains isn't up to the task. With a few rare exceptions, however, the revived SS troops have no particular love for Nazi ideology, and those exceptions for the most part wound up dead by the time of The Tuloriad.
Nimdok from I Have No Mouth and I Must Scream is a former Nazi doctor who worked alongside Joesph Mengele. AM's simulation puts him in a concentration camp and tasks him with bringing a golem to life to exterminate the "Lost Tribe," and he can either go through with it or redeem himself by relinquishing control of the golem to the Lost Tribe. Who, as he is fully aware, will promptly kill him for his crimes.
One Creepypasta entry features a Nazi medic as the protagonist. He and his group are sent out in true We Have Reserves fashion, and he goes insane trying to keep them alive on the Russian front with no resources, eventually dying after using his own blood to give a blood transfusion to his patients. The kicker is he's just a rudimentary doctor from a small farming community, and is completely uninvested in Nazi ideals, making this a rare case case of a Nazi protagonist being the hero. This is also Truth in Television as, by that point in the war, all capable German men who were physically capable were being put on the frontlines as Germany ran out of the aforementioned reserves.
The Hitler Rants, being a direct spoof of Downfall, naturally uses this trope as well. Not all of them though; only when the focus is specifically on Hitler and his staff.