Before Neo was found by the rebels did he not think he was using the machines, rather than vice versa?
For a post-modern, probably nothing. After all, one of the tenets of post modern thought is that there is no objective reality therefore there's no good reason to consider the rebels view of reality instead of Neo's.
But I think I'll take objective reality as a given. In that case the difference is how aware Neo is of reality. In the Matrix Neo isn't doing anything real, he's performing meaningless actions like rats in a laboratory maze. His activities are purely arbitrary and effectively decided by others. However, there's no fundamental reason that Neo's actions in the Matrix couldn't correspond to real world activity. Many tasks (and more as time goes on) could be done as well in the Matrix as in "real life". Almost all engineers, for instance, could do all of their work in the Matrix and in a far safer manner. Molecular biologists could "shrink" and manipulate cells and biologically active molecules "by hand" in a Matrix (the latter is something that's actually being worked on today).
So the essence is, are the people in the Matrix aware of their state? Do they know what they are doing? Neo doesn't, but those in my scenario do. In addition, in my view people chose when and how to be in the Matrix, they are not fooled / coerced in to doing so.
This is really quite analogous to the state of the rebels. Are they enslaved by the Matrix? Yet they enter it in order to affect change in the real world (if nothing else, to pop Neo out of his pod). So if one believes that being in the Matrix is instrinsically enslavement then even the rebels fighting against the artificial intelligences is enslaved. I don't see it that way. The rebels are not enslaved, even when they are in the Matrix because they are aware and they have made a real choice based on that awareness.