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Yeah, it's just like Python, which was named after Monty Python, but for some reason their logo is a pair of snakes. What does that have to do with a British comedy troupe?

Just take a look at the official Rust logo: a rusty metal gearwheel. I think they moved away from the “fungus” meaning of the name years ago.

The rust fungus gets it's name because it's colored like iron oxide - that is like the plants are rusting. If the fungi's name itself is a metaphor for corrosion/oxidation, why would it be improper to honor that theme?

It makes a lot of sense, since corrosion rust is a homonym for fungus rust.

Also this allows a wide range of topics - related words - to work as wordplay.