I'm not really qualified to talk about the pop-culture aspects of it, but I can say something about the academic approach to the Wehrmacht vs. the popular understanding of it. The trend you're describing is called the "Myth of the Clean Wehrmacht", which has been a prominent theme since the end of WWII. This wasn't an accident; many former Wehrmacht officers and soldiers actively promoted this idea in their memoirs because, frankly, it benefited them personally and professionally to do so.

The myth started with the so-called "generals' memorandum" that was written in November 1945 by Franz Halder, along with a few other Wehrmacht generals (notably Walter von Brauchitsch and Erich von Manstein), and submitted prior to the beginning of the Nuremberg Trials. The memo portrayed the Wehrmacht as an essentially apolitical fighting force, and claimed that the atrocities on the Eastern Front were solely attributable to the SS. Halder didn't get the idea out of thin air either; it was suggested to him by William Donovan, the head of the OSS (and later the CIA). By this point, the West was shifting into the Cold War mindset, and the military and intelligence knowledge of the former Wehrmacht leaders was valuable, so Donovan decided it was in the Americans' interest to whitewash the actions of the officers he believed were going to be useful. And indeed, many of the Wehrmacht's surviving generals took on prominent roles in the West German military. Konrad Adenauer himself encouraged this rehabilitation, making it a precondition of West German rearmament.

During the Cold War, Halder took over the German section of the US Army Historical Division, where he got to work proliferating this constructed image of clean, apolitical Wehrmacht. He created a large-scale history of the Eastern Front, including testimony from a number of Wehrmacht personnel that fit his narrative. His efforts were bolstered by other German officers who wrote memoirs during the 1950s that either focused solely on operational aspects of the war, excluding the political dimensions entirely (e.g. Heinz Guderian's Panzer Leader) or were explicitly exculpatory, claiming that the Germans' military failures and the atrocities the Germans committed were solely the responsibility of Hitler and the SS, while the Wehrmacht leadership had opposed Hitler (e.g. von Manstein's Lost Victories). Notably, Halder, Guderian, and von Manstein had all fallen out with Hitler at one point or another during the war, so they had an additional incentive to portray himself in a negative light (and, by extension, themselves in a positive light). These writings became quite popular in translation in the West, both among military personnel (Guderian frequently met with British veterans on friendly terms to discuss the war) and among the general audience that consumed popular history of the war.

The "myth of the clean Wehrmacht" remained the dominant narrative for the first quarter century or so after the war, and didn't really start to get pushback from academic historians until the 1960s, when a younger generation of historians started publishing more critical works, and the debate didn't come to prominence until the 1980s. It's worth noting that even at that time, German authors (many of them veterans) were still publishing exculpatory writings, particularly those with ties to the political right, like Franz Seidel. However, German historians had begun to publish books documenting the Wehrmacht's involvement in war crimes. Hans Adolf Jacobsen's book on the SS in 1965 and Klaus-Jürgen Muller's book on the Army's relationship with Hitler were two of the first to deal with the subject. I would say the dam really started to break in the late 1970s and early 1980s with Christian Streit and Alfred Streim's books on the mistreatment of Soviet POWs, which were some of the first to directly deal with war crimes committed by the Wehrmacht independently of the SS (and I'd like to point out that neither of these books has been translated into English even to this day; I'll come back to this point in a moment). It was also around this time that the Military Research Office began publishing the first comprehensive, critical history of the Wehrmacht that wasn't based on the myth.

This new trend created some tension between right- and left-wing historians in Germany over both the memory of the war and larger questions of German history, which led to the famous Historikerstreit ("Historians' Quarrel") in the 1980s. It's well beyond the scope of this answer to explain the entirety of the Historikerstreit (I took a class in grad school that devoted an entire semester to it), but it was in many ways the seminal moment for "modern" German historiography. The right-wing historians, led by Ernst Nolte, claimed that Germany did not need to feel any particular shame over its past, and that the war and the Holocaust were not unique historically; the left-wing historians, led primarily by Jürgen Habermas (and a few others) countered that Germany had taken a unique path (Sonderweg) that led to Nazism and the Holocaust, and that those events were unique and Germany couldn't celebrate that era of its past. As I said, this is beyond the scope of a reddit comment; if you'd like to read more about it (in English), I'd recommend Richard Evans' book In Hitler's Shadow.

The real turning point between the old, myth-based understanding of the Wehrmacht and the modern, critical understanding is the Wehrmacht Exhibition (Wehrmachtsausstellung), which was created in 1995 by Hannes Heer (who published a recent book on war crimes that I highly recommend if you read German). It spent four years touring Germany and Austria, showing hundreds of graphic images of war crimes committed by the Wehrmacht. This is the point where the dam broke, I would say. The Wehrmacht Exhibition put unquestionable evidence of Wehrmacht war crimes in public view, the same way it had been done with the concentration camps decades before.

In the era since the Wehrmacht Exhibition, there have been numerous studies published documenting Wehrmacht war crimes, including the mass murder of Soviet POWs and the direct involvement of Wehrmacht personnel in the murder of Jews on the Eastern Front. The myth of the clean Wehrmacht has been relegated to the extremist fringe, and isn't taken seriously by modern historians of any repute.

However, this shift in the academic history hasn't necessarily been transmitted into the popular historical sphere, and non-academic audiences are often not aware (or not fully aware) of the extent of the Wehrmacht's crimes. Part of the issue is that many of the best works documenting these war crimes haven't been translated into English; as I noted above, Streit and Streim (say that five times fast) published seminal works on Soviet POWs in the late 70s and early 80s, and those works still haven't been translated into English. I've worked extensively on the subject of Soviet POWs over the last few years, and I can tell you there's basically nothing in English on the subject. The other issue is that much of the popular history still falls into the trap of following Guderian's trend and focusing on the operational aspects of the war to the exclusion of the political and genocidal dimensions; most of the engagement with the political sphere is focused on the OKW's conflicts with Hitler over strategy, glossing over the intimate involvement of the OKW in planning and executing a war of extermination on the Eastern Front. I don't think this is really deliberate obfuscation in the way it was for the German generals in the post war, more of a blind spot for military historians who are used to focusing on strategy and tactics rather than politics and society. That trend has taken a while to undo as well, and it's still an ongoing shift in the world of (academic) military history.

If you want to think about this in another, maybe more familiar, way, I would draw an analogy to the Lost Cause of the Confederacy in the United States. That myth started right after the war with the surviving leaders of the Confederacy who wanted to whitewash their legacy, was carried on both by historians and by ordinary people who wanted to protect their forefathers' names, and made it into popular history, where it continues to exist even though people may not realize it because they focus too narrowly on the military dimensions of the war.

Sources:

The main source I drew on for this answer was Ronald Smelser and Edward J. Davies' excellent book, The Myth of the Eastern Front: The Nazi-Soviet War in American Popular Culture, which looks at the popular-culture dimension as well as the academic-historical one. I highly recommend it, since it fills in some of the blind spots I wasn't able to adequately address here.

As for direct academic correctives to the myth of the clean Wehrmacht, the original one in English is Omer Bartov's The Eastern Front, 1941–1945, German Troops and the Barbarization of Warfare (St Martin's, 1986), which is excellent. A couple of more recent books that have been translated to English are Wolfram Wette's The Wehrmacht: History, Myth, Reality (Harvard UP, 2007) and Rolf-Dieter Müller's Hitler's Wehrmacht, 1933-1945 (UP of Kentucky, 2016).