The matrix made him only think he was a programmer.

Why do you say that? Just because the humans plugged into the Matrix are given false stimuli does not mean that they are unable to perform actions of their own volition, even write code, just that the events pertaining to and consequences resulting from the actions would be represented in a virtual environment. The very fact people can be retrieved from the Matrix and go on to adapt in short order to the real world IMO indicates that their experience as brains in vats includes intentional actions. Is it really believable that the human brain grown entirely in a position of passivity could be retrained in adulthood to carry out actions?

I've always interpreted the Matrix as a form of symbiosis in which the machines rely upon humans for energy (silly really, why not use cows?), and humans are permitted to live virtual lives indistinguishable from the real thing in enchange. It's quite conceivable to me that the individuals inside are by and large free to build a world from their own desires and ambitions. Neo may well be a real programmer, using a language every bit as real as Perl, with the caveat that if Decartes is correct and it's possible that an evil genius could convince someone that 2 + 2 !=4 then by extension, for example, Turing completeness could mean something different in the Matrix. But more than a few people disagree with Descartes on that point :)

Update: Ooh, fuel for the fire: Trinity hacks! :^)

Remember Cypher, who sold out? We wanted to go back to the Matrix, and one of his demands was what he would be when returning, indicating it's the Matrix what decides, and not the human.

And the Matrix isn't living in symbiosis with the humans, because a symbiosis is benefitial for both sides. Clearly this isn't the case, unless you want to see Neo and his comrades as highly evil people. The Matrix seems like a parasite, draining energy from the humans (they might use cows as well), with nothing real in exchange.

Morpheus compared living in the Matrix with experiencing a dream.

Abigail

symbiosis is benefitial for both sides.

Bah. There are 3 types of symbiotic relationships: mutualism, commensalism, and parasitism. In mutualism, both organisms benefit; in commensalism, one organism benefits and the other is unaffected; in parasatism, one organism benefits and the other is harmed.

Therefore, even if the Matrix is parasitic, it is still a symbiotic relationship.

And the Matrix isn't living in symbiosis with the humans, because a symbiosis is benefitial for both sides.

In biology, symbiosis can refer to any two (or more) creatures in a relationship. It is not limited to cases where both creatures are benifiting (mutualism). There is also parasitism, where one creature benifit and the other is harmed. And there is communitilisim (can't remember if that's the right term), where one creature benifits but the other isn't directly harmed.

Spolier for Matrix Reloaded below. Read at own risk.

Notice when Neo is talking to the high council member in the engeneering section of Zion. He brings out that humanity's survivial is tied to machines those, but other machines are trying to kill them (but not really, since those machines also need humans for their survivial, at least to some extent). (This also goes into Morpheous' comment in the first movie that humans have always relied on machines for survivial). So humanity is, in one sense, in a mutalistic relationship with the machines, and in another sense are the parisites, and in yet another sense are the hosts for parasites.

----
I wanted to explore how Perl's closures can be manipulated, and ended up creating an object system by accident.
-- Schemer

Note: All code is untested, unless otherwise stated

That plot about the energy was so outstandingly stupid, even comparing to other parts of the film. You could think it was just a disguise to some other depths of the mystery - but there was nothing else that would feed this theory, so it would lead you to nowhere.