Actually, sesse is completely right. The guitars in FLCL are definitely an allusion to penises (so are the bats, and the things that come out of naota's head).
kiss_army, a 12 year old boy's life is all about penises. It's their hormonal prime, they're going through puberty, and sex is always in the back of their mind. That's what FLCL is about.
For example, in episode 5 Haruko goes into a minute-long rant about guitar skills before pouncing Naota down on his bed in some what of an erotic position.
Naota: "It's dangerous to go waving that thing [her guitar] around."
Haruko: "Use your guitar again. One more time, Ta-kun. ... Kaking ... You did it so great last time."
Naota: "Not interested."
Haruko: "[giggles] I should teach you how to be a man, Ta-kun."
Naota: "Yeah, like you know!"
From the dialogue and positions in this scene, "guitar" is obviously implying "penis."
I'm working on a complete analysis that will explain a lot of the metaphors in FLCL - it will be on the site when I'm done..
Feel free to argue this theory.