In addition to all of the (very interesting) interpretations given above, I think I have another one. The way I see it, the point of the movie is that the protagonists and antagonists are backwards. Morpheus is the real villain, and the movie is about how good people can be persuaded to do bad things.
Morpheus is the head of a group that I think could most accurately be described as a terrorist cell (though they would call themselves freedom fighters). They are part of a huge network of people whose main objective is to bring down 'the system', and they don't give much thought at all to the people they hurt along the way, or what will happen if they succeed.
Morpheus' entire philosophy seems to be based on his belief that the 'real' world is essentially better than The Matrix, due to it being more 'free', although he acknowledges that there isn't any perceivable difference between the Matrix and their own world (before it was destroyed, that is). We can take it as an axiom that more freedom is a good thing (all else being equal), but the 'real' world is pretty obviously a worse place to inhabit than The Matrix. In the 'real' world, people are forced to live underground, with recycled air, water, and (presumably) food. They never enjoy sunlight or nature's beauty, and cannot leave as long as they want to live. On the other hand, in The Matrix, people can travel the world and see all the wondrous things that existed before Earth became an inhospitable desert, and standards of living are generally far higher. One could say that a gilded cage is still a cage, but here we are talking about a cage that extends to the edges of the accessible universe, at which point it stops being what we could reasonably call a cage. Morpheus talks about a 'prison for your mind', but as far as we are told there is no mind-control or brainwashing going on in The Matrix, just the provision of a nice place in which to live.
So Morpheus and his crew are trying to destroy The Matrix, because they either haven't looked around themselves lately or are deluded, and along the way they kill dozens, if not hundreds, of innocent people. All those police and security guys in the building where the agents were holding Morpheus, plus who-knows-how-many more before the events of the movie began. They justify this by saying that the people in the Matrix are all potentially agents, so they're all enemies, despite these being the same people that they are trying to 'save'. Along with being contradictory, this is exactly the kind of absolutist, with-us-or-against-us rhetoric that irrational extremist groups use. There seem to be no shades of grey in Morpheus' eyes, and he feels compelled to impose his values upon the world, whether the world likes it or not. And anyway, what is their plan for the world after the Matrix is destroyed? At best, they'll end up with 6 billion angry, half-crazed people with festering plug wounds who couldn't possibly be fed or housed in Zion. At worst, all of them will die when the Matrix is shut down, and the 'real' people will be the biggest genocidists in history.
The machines, on the other hand, have almost completely ignored the humans' past attempts at committing genocide on them, in favour of a symbiotic relationship that makes everyone many times happier than the 'real' world could. When the humans destroyed their own planet, the machines provided them with a replacement. Although the machines did this for their own benefit, there is no reason why they couldn't have made The Matrix just as miserable as the 'real' one, but they didn't. They do not interfere with the people's lives, except to protect them from the people who might accidentally pull the plug on everyone.
So we meet Neo. He's a bright, young, curious guy who has a crappy life, is victimised by authority figures, and reads about conspiracy theories on the internet. Morpheus appears and asks him to leave his life behind, with only promises of the truth (the objectivity of which is undermined by the existence of the matrix anyway) and no mention of the possible consequences. The whole thing is very romantic, which helps both Neo and us get caught up in the conflict without giving it too much thought. And this is what I think the movie could have been about: we come to respect Morpheus and hate the machines just as much as Neo does, because we only see one side of the story. We, like Neo, are lured into siding with the irrational extremists.
I don't think that this is how they wanted it to be read, or that they intended for it to be ambiguous in this regard. The fact that the people in Zion have beautiful multicultural families and the Agents are stiff white men in suits and dark sunglasses makes it seem very clear to me that the machines are supposed to be the baddies. But what confuses me is that they wrote in Cypher's deal with the Agents, where he decides that he prefers The Matrix to the 'real' world — this means they'd given some thought to this idea, but then they completely disregarded it. Are they that hung up on the idea of freedom at any cost that they forgot what freedom is in practice? I don't know.