So here's my spin. Obviously, as apostates we're like the people of Zion in the Matrix... all of us have been extracted from the "matrix" of the Watchtower cult. Neo is like Jesus, obviously, as he's "the one" people put hope in and the people in Zion who don't believe in Jesus are like apostates who left the religion but don't believe anymore.
Morpheus is like all the apostles rolled into one, I think, but I am open for debate on Morpheus. The "Architect" is NOT Jehovah or God or whoever, but is the Watchtower Bible and Tract Society as he created the world of the Matrix. The Agents, those are elders because they're trying to rid the matrix of all the ones who won't assimilate. Agent Smith, this time around, is like the Witnesses who haven't DFed or DAed yet, as he is still in the matrix but is malfunctioning and contaminating other agents.
In the Matrix Reloaded, Neo and the others go to the Oracle for advice, and she says they need to go find the keymaster, but he's being held prisoner by Marivingian (sp?) which is this evil corrupt program in the Matrix. They commented that he was once like Neo but then he changed... that's like an apostate who left the Borg and was normal for a bit but then went drug crazy and nutty etc.
I have more, and more, and more, and more, and more about this subject as it is going to be my masters thesis at some point in my college philosophy career... so If you're interested in debate, let's have it folks. ^_^ Isn't it just creepy as hell, the similarities?