There's a couple reasons for the Lovers being red, blue, and green.
The personal, and initial one, is that I'm in a triadic relationship; this is why I drew three Lovers in the first place! We have a few playful metaphors for ourselves, and they tend to end up with those colors as part of the symbolism.
The visual one is that I wanted them to all be about as bright as each other. I did try making them red/blue/yellow, but yellow is innately a lot brighter than blue and red; the yellow Lover either became the focus of the whole image, or looked dirty and unpleasant when I darkened her.
The deeper visual reason is that R/Y/B aren't the only primary colors - they're just the subtractive primaries, of reflective pigments. R/G/B are the additive primaries; if you add red, green, and blue lights together, you get bright white. If you mix subtractive primaries, you get mud.*
Waite makes this card about the Eden myth and gender duality; Crowley makes this card about... um... my, he does go on about this one, doesn't he? Creation and sex magic and duality. Most of the duality-themed cards, in my hands, become invitations to transcend dualistic thinking, to look off of the single black/white, yes/no, male/female, true/false dimension and into wider realms of possibilities. (Note, thus, the black and white hands reaching up for them!)
* If you look deeper into color theory, you will discover that "red, yellow, and blue are the subtractive primary colors" is, in part, a lie. Four-color print process uses cyan, magenta, yellow, and black. And if you shine red, green, and blue lights on a white surface, then turn off the lights in varying combinations, you get... cyan, magenta, and black. Mix CMY inks together and you get something closer to black than the muddy color of RYB paint. It's still not pure black, mostly due to our inks not being absolutely perfect in their absorption spectra, so printers add the black ink. Plus of course we do like black text on white paper a lot and it's pretty awkward to print the same text three times.
My, I do go on.