FLCL revolves around Naota, a young boy living in a quiet town. He spends his days living out the same routine over and over, until a strange woman runs him over with a Vespa. At this point, things take a turn down a more interesting path for the boy, however one that he is not quite in control of. From the very beginning, Haruko is manipulating Naota for her own needs, and she's not the only character trying use the boy for their own desires. Manipulation is a big part of the Fooly Cooly world, touching upon some innate human selfishness, and how easily one can fall for fake love.
Naota is a key to getting what Haruko wants, and she is not afraid to use any means to get to Atomsk. She easily integrates herself into Naota's household by taking advantages of his lecherous father, even going so far as to replace him with a fake to serve her needs better. From this point she is closer to Naota and closer to her goal.
Of course, Naota is not willing to comply so easily, and she takes advantage of his innocence, using seduction to push him in the direction she wishes. Naota eventually falls in love with Haruko, making it much easier for her to string him along. He becomes so strongly infatuated with her, that even when the truth is revealed to him that she has been using him and does not actually care for him, he still clings to her, or rather the memory of her after she leaves him. Love becomes a key tool for Haruko's plans, she does not care about the boy, she only cares about her own selfish goals.
Another character who attempts to manipulate Naota is Amarao. While he does not use any direct, underhanded, means, he still tries to reach his goal through Naota. Amarao does see a part of himself in Naota, a part that seems to have once loved Haruko. He is now driven to stop her, and attempts to “warn” Naota of her plot, while simultaneously trying to push his own ideals onto the boy, to try to sabotage Haruko's plan. He seems to be the only character who does not actively try to manipulate Naota's emotions, however through Amarao we can see how easily such emotions can be twisted to spite.
Mamimi is not as manipulative as the two above, but she still does attempt to manipulate Naota. Mamimi still clings to her affection for Naota's older brother, not knowing or possibly denying that he has left her behind. Without her love there, she uses Naota as a replacement, the “next best thing” in her eyes. Even as he ignores her advances, she still attempts to push herself onto him, claiming that she will “overflow” and that “something bad would happen” if she did. When she is left behind by Naota, her replacement “Ta-kun” becomes the small dog-like core. Driven mad from the abandonment, she attempts to use this new “Ta-kun” to get revenge on all those that had wronged her.
Naota is even prey for the manipulations of minor characters, most noteably Ninamori. Not only does she tamper with the vote to put herself in the lead role of a play with Naota as the secondary, but she adamantly pushes this role on Naota despite his protests. There are also several instances where she appears to be trying to seduce Naota, however these attempts are always cut short by Haruko.
Inevitably, Naota is just one boy with the world around him trying to shape him to their own goals. They play with his emotions, pull him in their own directions, and treat him as nothing more than a stepping stone in the path to their goals. It seems to be how many people view others in the world, either obstacles or tools. If a person is not useful in helping to reach your goal, they are usually in the way, or at least in the view of the greedy.