By 1945 National Socialism was utterly discredited in Germany. Any comparisons to occupied France etc fall down because of this. Germans just wanted food, peace and "normality".
Unlike the Japanese with their Emperor cult and Western countries with their democratic traditions...even the Soviets had their ethic of communism...Germany in 1945 had nothing..utterly bankrupt in ethics, philosophy and nationalism.
Resistance would have had no basis of support.
I don't think the general populace would have been fighting for Nazism (which indeed was a bankrupt ideology by then). But rather to protect themselves and inflict harm on brutal invaders, as the Nazi's already had recognized with their Volks~ appellation to everything they could think of in the latter part of the war.
Everybody wants food, peace and "normality", the conquered masses of 1940 Western Europe as much as the equally conquered masses of 1941 Eastern Europe. But if they are faced with oppression and indiscriminate killings in reprisals, everybody takes up arms as happened during WWII. The Germans would not have been any different in similar circumstances.
A resistance movement in Germany was therefore a genuine concern in allied circles and a major effort was planned to prevent this from happening, from making use of low level local officials (even if they had been die-hard Nazis) and a relatively gentle occupation to distributing food and supplies to keep the Germans content with their lot.
That is why Werewolf struck such fear in the allied high command. It would mean that such "gentle" measures would not be possible which would inevitably lead to rising anger within the wider German populace as they suffered under harsh counter-insurgency measures which always work on "collective guilt" as it usually is impossible to pinpoint the actual perpetrators as long as they are supported and shielded by the general public. A resistance movement in occupied Germany might well have risen and become a long-term problem for the allies, irrespective of its original starting point.
Nobody was looking forward to that. But that doesn't mean it couldn't have under the right circumstances.