not only humans are slaves in the matrix

The programs inside the matrix as well.
Their as much taken from "reality" as the humans, forced to work (and live, because the agents don't ever seem to take a break ;-)) inside the matrix. They never get out being programmed in it.

These are my thoughts about that, take them as you will:

Some of these programs inside the matrix are aware of their limitations, of their so called "freedom", they would like to get out of there; have an existence of their own, would like to be programmed into some kind of "body" so they could feel free.
The human body's are held in the pods and subsequently their minds are held.
The programs inside the matrix are programmed in the matrix and subsequently have no body outside it and subsequently their "minds" are held as well.
They are actually in the same position:
SLAVES of the system.
Programs that seem to understand the limitations (the imprisonmental state) of being a part of the matrix:
*Smith
*The oracle
*Merovingian and friends

They just seem to have a different opinion in how to do something about that situation:
*Smith: take over the matrix and the real world by "infecting", which would eventually lead to a system crash, because a viral infection ruins a lot but doesn't realize that in the end total control would be the end of it....and he would still not be free from the matrix even if he had totall control of everything happening INSIDE, he would still be trapped inside.
*Merovingian and friends: they don't accept being deleted, they remain in the matrix, they rebel, but they don't escape the manipulated reality of the matrix. They choose, like Neo, only what they are allowed to choose: exile ór staying, they don't have the choice for real freedom either.
*Oracle: being an intuitive program (YES, I think she's the mother), she is able to understand the reciprocal dependence man-machine, machine-man much more than a not intuitive program as Smith, who's just going nuts in taking power wherever and whenever. The oracle might be designed to study human behaviour and set up the prophecy to control the one (and with that: all the free people eventually) but because of here learning she has come to an understanding of the only long-term solution for both sides (man-machine)
The prophecy might be originally been set up , but now the oracle seems to want to convince the one about the importance of working together, by giving him insight in how limited the system of choice is.

The programs often make remarks that make it clear that they know about the limitations of the choices:
"The Oracle: We're all here to do what we're all here to do."
"Smith: Thank you. But as you well know, appearances can be deceiving, which brings me back to the reason why we're here. We're not here because we're free, we're here because we're not free. There's no escaping reason, no denying purpose - because as we both know, without purpose, we would not exist."
"Merovingian: No. Wrong. Choice is an illusion, created between those with power, and those without"(note: he might have a lot of power, but that's only inside the matrix, he's still accepting that and just enjoying the ride)
"Keymaker: We do only what we're meant to do."


Referring to the fact that they are all part of the system, they are programmed.
It seems to me the oracle wants to help, for the sake of man and machine.
She realizes that she can never be free without humanity being freed, and working together.

Being a program in the matrix gives you just as much limitations and "illusions" of choices as it gives the humans.
Don't we ALL (that is creatures with self consciousness man ór machine) just want to be free????
I think that will be where the third movie will go.

I think that maybe programs like the Oracle and the Merovingian see the rebels fighting for freedom and that is why they want it. If you agree with a lot of the threads on this site, then you'll probably already think that the Oracle and the Merv. are exile programs, who have to be careful not to get caught and be deleted. They might want freedom, but it's not the same kind as what the rebels are fighting for.
What would a computer program do with freedom? If the computer didn't exist, neither would the program- Merv, Oracle and Keymaker would never have been created, and if the matrix was destroyed, they would cease to exist.
The programs can never be free, because they were created with a purpose. It's only the rebels that have anywhere to escape to.

I understand what your saying, but
You said:
"What would a computer program do with freedom? If the computer didn't exist, neither would the program- Merv, Oracle and Keymaker would never have been created, and if the matrix was destroyed, they would cease to exist."

Exactly!!!! And thats what they don't like about it. That's why they hide and/or rebel. But however, if they work together with humans, they could work in "the real" world. They could all get out of the matrix. And a new "job" (purpose) for these programs could be found. They could even get a machine (body) of their own, if they were programmed into one. The oracle clearly states: "The only way to get there is together"
I think because she wants to be free as well.
AI, programs with self consciousness realizing that they are being kept prison by the Matrix. Just like Bi66er realized he was a slave as well. Why would it be so impossible for these programs to want freedom? Even the simpler version of Bi66er wanted to make up his own mind.

"The programs can never be free, because they were created with a purpose. It's only the rebels that have anywhere to escape to."

I understand what you mean, but that doesn't mean that they wouldn't like to have a different purpose (/life)
In my opinion they could be free (well free-er at least) if some new government would rise; a government of man and machines, a democracy. Not this dictatorship that the Matrix is for all it's inhibitants. They want to be free, a lot of them clearly don't like the purpose that's forced upon them. They might want to long for the freedom of choice just as much as humanity does.
The whole movie is about freedom of choice, and AI (in this movie) clearly seems to have a notice of their mental prison.

Just imagine being a program inside the matrix realizing that you are stuck there, assuming AI is capable of thinking counsciously, like us? Wouldn't you be frustrated?

well, yeah, it seems dubious that the wachos. can anihilate/destruct a matrix and all the programs inside, that would looks like a genocide after all that they showed us in the movie.
the only way i could see all progs destructed was if both worlds ends in M3, on which i already know that Warned Bros would never have accepted to produce it.
the only logical guess left would be a reset of the matrix with an agreement/peace between Humans/all programs or Humans/some programs.

wow that is some interesting stuff