I apologise in advance for the length of what follows!
I think animation has a long history of dealing with fascism in different ways. In the 1980’s, storytellers were obsessed with the military machine. They were in the depths of the cold war and it had been only 40 years since the fall of the Third Reich. Thus so there was no discourse between GI Joe and Cobra. Megatron was nothing but a despot who kept his followers in line with fear. Lion-O was even a child soldier, forced to the front lines before his time.
I can’t comment much on the 1990’s as action cartoons kind of fell out of favour after Ninja Turtles. We were made however to cheer for a duck who hoarded all his wealth and probably didn’t pay much tax.
Of the last 20 years though?
Ben 10 managed to stop the High Breed, a xenophobic race of ubermensch aliens from wiping out all other ‘inferior’ life forms by helping them. They took the fight to them but chose at the end to unleash a wave that combined their sterile, ‘pure’ DNA with that of other species. The war was ended thanks to the joint efforts of Ben Tennyson and a High Breed warrior he had befriended in a classic ‘we must team up to survive’ episode prior.
The pinnacle of animated TV shows, Avatar: The Last Airbender starts out by painting the Fire Nation villains as bloodthirsty, imperialistic conquerors. By the time we get to season 3 we see how propaganda is used in schools within the Fire Nation itself and that the people are just products of a system. By the end the despotic Fire Lord has been deposed by his son who, having seen what a century of war has really done for the world calls a truce. There is then actually quite a lot of sequel material that shows that bringing peace and balance to the world is not so simple but it starts with words of kindness and a willingness to forgive.
Consider this: had Woodrow Wilson never caught a debilitating case of Spanish Flu he would have been able to act as the voice of reason in drawing up the Treaty of Versailles. France and the UK would have not got their pound of flesh and Germany would not have suffered so badly in the inter-war years which directly led to the rise of the Third Reich.
In other words: we could have defeated Nazism with kindness before it ever got off the ground.