It's one of those cyclical things. You know, like the hydrologic cycle... or like a cat chasing its own tail.
In the first scene we start with Trinity and Cypher talking while the camera zooms inside of a monochrome monitor and into the Matrix. At the end, we hear Neo talking as we again zoom into the Matrix, this time to look at Neo talking to…whoever he's talking to, it's not really clear. The machines? The agents?
At any rate, Neo's telling it like it is. He's going to show the minds trapped in the Matrix the truth, or at least the lack of truth. Again, very unclear exactly what he's planning on doing.
He then hangs up the phone and steps out of the phone booth like a bona fide superman. He even flies like superman with his fists outstretched above his head like he's riding a motorcycle that is way too big for him. But maybe that's just how one flies: who knows (not us, unfortunately)? The point is, Neo's the man now, and things are about to get revolutionary.
So, to answer the question: what's up with the ending? Neo is. He's up, up and away.