for multiple episodes they showed him as a cool guy with a good cause, but then randomly made him a villain with no reasonable motivation

Oh they gave him the Marvel Special

I think he only shows up twice. First time he’s protesting random trivial crap, second time drilling oil

More likely explanation is that "he had great ideas but did them the wrong way" is the leftmost message the lib writer could conceive of making about Che

That's how all revolutionary figures are shown in liberal media. Usually, the go-to is to create a character with good intentions, a practical mindset for achieving change, and enough of a material base for an uprising, but have to character assassinate them by arbitrarily making them evil in some manner, jumping the shark.

It is extremely difficult to make a sympathetic, well-written revolutionary villian, because if the audience isn't reminded to hate them they will side with them.