Because the North was wishy-washy on how they actually wanted to respond to the aftermath of the Civil War.

The South lost a lot during the Civil War, namely their primary economic driving force: slavery. Though sharecropping was instituted essentially immediately afterward, which minimized the effects to a certain extent, basically the entire Southern economy suffered immensely; additionally, because the vast majority of the battles were fought on Southern soil, southern economy and infrastructure was devastated. Their voting rights were also taken away: Radical Republicans wanted to punish the South for starting the Civil War, so they passed a law saying no southerner could vote if he had taken part in the rebellion against the Union. As we can see with every suffering society throughout history, when people are suffering economically and feel they have no "voice," they look for someone to blame. The South blamed the people they felt were responsible for their situation: black people and Northerners. Thus the animosity the South felt towards the North never dissipated and they were not particularly inclined to accept anything the North was willing to give them or do for them after the war.

Sherman's March to the Sea where he and his men burned and destroyed everything they came across didn't help either. He basically singlehandedly destroyed the majority of Southern infrastructure, including railroads, farms, and possible economic solutions to the problems posed by the slavery issue. The effects of his campaign were literally devastating for Georgia in particular; even 150 years later, they still haven't truly recovered in some places from the destruction and havoc wreaked by the March. While it ultimately greatly contributed to the Union winning the War in the Deep South, the impact left deep and lasting ramifications for everyone left behind.

The North then didn't really interfere politically, socially, and economically to the extent that they should have during Reconstruction; they basically imposed martial law and instituted several really harsh punitive measures, then left the South alone for several years (leading to the installment of the "black codes"), then tried to come back again, which of course was their biggest mistake. Then they helped out for a bit, then pulled out again. Even Johnson himself sent mixed signals, pardoning 13,500 of the 15,000 less-wealthy Confederates who applied (he blamed the upper class for secession) but forcing Southerners to default on their war debt, thereby ruining their credit so they couldn’t fund a second rebellion. The continual waffling and half-hearted attempts to actually help the South rebuild hurt way more than it helped. Like...economy and land wrecked, their largest city and transportation hub (Atlanta) burned to the ground, their main economic driving force (slavery) gone, morale being affected by the fact that they'd lost the war, and then a flaky federal government that fought a war to keep them as part of the country then refused to help them...yeah, not the best circumstances under which the South would actually accept Northern help or ideas about how to run their society.

There's a lot to be said on the topic of whether Lincoln's views on attempting to fully re-integrate the South vs. extensive and long-lasting punitive measures to punish the South for leaving the Union would have been "better" for the South, and I don't really have much of an opinion either way as both viewpoints have excellent arguments to prove their point (except being from the South I would quietly observe that enforced full integration and a closer federal watch on the region might have prevented some of the more heinous laws and acts regarding the treatment of black people that occurred during the Jim Crow era instead of the "live and let live" attitude that was adopted at various points during and after the Reconstruction period). More than any one way of doing things there needed to be consistency with how the North treated the South after the war; since the Union was basically evenly divided between those wanting to enact "full forgiveness" of the South and those that wanted to raze the South to the ground and punish them severely for their actions, such consistency was simply nowhere to be found.

The lack of a consistent "Southern policy" led to a sort of half-hearted "hands-off" policy post-Reconstruction that let the South basically govern themselves, which was their way of "forgiving" the South for trying to leave: "Okay, we'll let you govern yourselves to an extent." This severely limited social integration efforts, as white Southerners were not only heavily disinclined to change the status quo but now felt the pressing need to do something about all of the newly freed black people who were "overstepping their bounds." Said newly freed black people really had no recourse, as the federal government didn't particularly care about them or their plight: as long as the South wasn't going to try and leave the Union again, the South had been cursorily "punished" during the initial phase of the Reconstruction, and slavery didn't technically exist, they weren't willing to get their hands dirty immediately after such a bloody and catastrophic conflict. They did just enough to seem like they were "punishing" the South without having to exert the consistent long-term social, economic, and political effort to actually change how Southern society operated. The Southerners took advantage of this position to bargain for the end of Reconstruction and install new, racist Democratic regimes that either ignored or encouraged racism, which basically put an end to all social integration efforts that had happened up to that point and led to the Jim Crow era.

America's lenient treatment towards the Nazis post-World War II is different for two reasons: one, the German people were willing to self-police and re-educate themselves afterward. There was an internal willingness to change their society and culture that the South did not have. America and the Allies also imposed a complete occupation of (West) Germany that allowed them to basically completely rebuild Germany from the ground up from an economic-political perspective; their policy was consistent, complete, long-term, and largely all-encompassing. The North obviously declined to occupy and enact this type of policy in the South (the closest they got was imposing Northern leadership on the South at the state level, which only led to more resentment rather than true social change).

Two, the circumstances of a country under an authoritarian dictatorship doing heinous acts towards their own people and waging war against other countries is an inherently different situation than an internal civil war, which carries a lot more internal cultural baggage for the groups involved. The enemies involved are not external (ie, the Allies, the Jews, and other ethnic, religious, and political enemies who weren't considered to be "real Germans") but internal ("America fighting against itself"), and thus often leads to various ways of dealing with the "losing" side depending on the civil war and country in question. Additionally, Germany in WWII was concerned with "purifying" their country through ethnic cleansing and racism while the South was concerned with keeping slavery alive and well; rather than trying to murder or expel black people en masse, they were trying to actively keep them not only in the region but enslaved. Different problems (wanting to kill/expel people vs. wanting to keep them enslaved) are not necessarily comparable and need different answers.

Basically: it wasn't necessarily that the North didn't punish the South for the Civil War enough or that they didn't pursue a policy of full reintegration and social change, but the fact that they tried to do both and neither simultaneously and ended up with a convoluted mess of a Southern policy that helped no one and only served to exacerbate the social and economic conflict in the region. Had the North been consistent in their policy (whatever that policy may be) towards the South until the South basically "got itself together," I conjecture we would have seen a much different outcome (of course, that is pure conjecture and has no real historical basis in fact).

Note: the problem wasn't necessarily Sherman's March itself, but the fact that the Union did nothing substantial to really help the South recover economically from its devastating impact afterward. Add that to the initial harsh punitive measures, the additional punitive measures post-1868 after letting the South essentially govern itself for three years, and carpetbaggers (rich Northerners who went South to profit off of the Southerners' misfortunes after the war) and you've got a hotbed of disaster. It's been proven time and time again throughout history that poverty and desperation lead to a lot of festering of hatred, and in the South's case, that hatred manifested towards the people it saw as the product of their misfortunes: Northerners and blacks. Social integration for said groups was thus basically impossible since they were being blamed for the social and economic aftermath of the Civil War in the South, thus it was punishment and not social integration that the Southerners sought in the post-Civil War era.

You can read a little bit about this wishy-washy "leave them alone or interfere" policy here and here, and West from Appomattox: The Reconstruction of America after the Civil War by Heather Cox Richardson is a good book to take a look at. A lot of this also comes from my own experience growing up in the South around several significant battleground sites (including the Battle of Chickamauga/Chattanooga) and several years of having Southern history taught in school.