Neo is a program, just like the Oracle. The Architect gave a hint that he was when he said that there was an "Anamoly with the Matrix code" that appeared everytime. How can Neo be an anamoly of a program code, if he's not a program himself? Also, the French guy from the restaurant used the keymaker to get the key to terminate the Oracle. Seraph protects something else other than the Oracle, something the Oracle knows about but only Seraph is strong enough to protect. Agent Smith is a virus, and his sole purpose is to erradicate Neo, but he's getting out of control and he eventually spreads all over the Matrix world. Basically everyone in the Matrix... All innocent bystanders get turned into Agent Smiths.