XKCD Isn't Funny - #1615 - Red Car
I kinda feel like this was a deliberate attempt by Randy to avoid being CouldBeATweet. It's a neat example of how word choice can affect stuff. Because we only get the information that the car is red through the art, the line only makes sense in the context of the full comic. In contrast, the alt-text is totally an example of CouldBeATweet, but it's okay, because alt-text.
That said, 'cyan' is probably the most pretentious color he could have chosen. It couldn't just be 'green', like we all learned on the color wheel, it has to be the precise RGB opposite. Maybe it's supposed to bring contrast between the relative high level of the word 'cyan' and the fact the comic's a dick joke, but I think green would be funnier too, since it conjures up a worse mental image.
I asked my furry friend* how he would feel about a cyan penis and he (and by extension all other furries) would be into it. The cyan penis would obviously be a point of pride. XKCD has failed to do the research yet again. For shame, Randy, for shame.
Also, wouldn't he be just compensating, not overcompensating? Like, red and cyan would neutralize each other, his penis wouldn't become more red than cyan. Compensating is even the more commonly used word.
This comic kinda reminds me of the bits he'd add into What If? articles. I can't imagine the question that would've been asked to make that image relevant, but I imagine I'd be both interested and disturbed. This joke really feels like a side thing, a one liner as part of a larger set of jokes. There's nothing offensively bad about it, but it's not exceptional in any way. As it is, it's essentially filler.
*Who, by the way, thinks this comic is "retarded" and "impossible [to rewrite to make it good]".