I actually find these questions interesting. These are the reasons I like the last Matrix movie: the lore is awesome.
1. He is a program. Think of him as the admin. But he is not the creator of the machines: the creator of the machines is humanity. They are controlled by the Deus ex Machina (big machine Neo sees in the end); some think he's the same thing as the Architect, others say he's not.
2. She is the Matrix. Or at least the current generation of the Matrix. There are three Matrix phases: the first one was a paradise where everybody got their heart's desires. But human nature could not accept this, and many "crops" died in the process. The second Matrix was based on "cause and effect" programming, and was considered the "Nightmare" Matrix where horrors lived in the world. The Merovingian is the Oracle-equivalent to the Nightmare Matrix, which he essentially governed as the thing that kept "order," but he is obsolete. The Oracle, now, is the "Choice" Matrix, where humanity is given an illusion of choice. It's also debated as to whether or not the Oracle was ever on anybody's side. She is another system of control; I'll get to that in a minute.
3. That is part of the illusion of "choice." The humans needed to believe they had choice.
4. They are the creatures that roamed the Nightmare / "Cause and Effect" Matrix. Some believe they are Agents who governed that version of the Matrix. They, along with the Merovingian, are obsolete and have been replaced.
5. He is a product of the machines. He and Trinity are part of the control; both are part machine, because the machines built them for just that purpose. Neo was created to reboot the Matrix, and therefore - because he was born with the Code - he was able to interact with the machines and see the Code in the Matrix. Trinity was created as a "safety" in order to give Neo another illusion of choice. But she and Neo were always meant to be together, because they were genetically created for that specific purpose.
Essentially, free will is a lie, and it always was in the Matrix. Neo, however, did defy the machines when he did not reboot the Matrix when he was supposed to.
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