Charlie, is not about a guy called Charlie. (though it could be, it can be anything)
It's about 'muse'...his muse, your muse. Creative soulforce.
Or as he explains the song (as he usually prefers not to do):
"That has a lot of stuff going on. The third part is straight love song: 'My heart, your skin, this love I'm in.' It's also about the power of not having to be right all the time. If you want to get along with somebody, let them be right, and it will last longer."
Fun fact, as the story goes, the band wanted Charlie to be released as a single, but the record company didn't go for it.
Being the rebels they are, they set up a contest in which fans could make a video for the song, and the winning song would be re-shot into the official video. Portraying the little Chili's running around L.A.
"My heart, your skin
This love, I'm in
We don't arrive without a surprise
You're right, I'm wrong
Be free, belong
Intimate sight has come in to light"
- Red Hot Chili Peppers, Charlie