It stands for "Centralized Processing Unit", but people tend to just use it as a shorthand for "computer". I imagine the first instance of that went something like this.
"We've gotta be careful, the CPU might overheat."
"CPU? Oh, I get it. ComPUter, right?"
*Sigh* "Yeah, sure. That's what the means..."
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Socran's Razor: "Never attribute to massive stupidity by someone else, what could be explained by a tiny bit of stupidity on your own part."