It's just one of the ways the film can be interpreted. Neo is Jesus (sent to sacrifice himself to save the world), Trinity represents the holy trinity and love, the rest of the crew on the ship are the disciples, cypher (who betrays neo) is judas, the matrix's creator is god, neo dies for the same amount of seconds or minutes as the number of days before jesus rose again, they all live underground and dream of going above all the dirt and smog (heaven). I think that's all the ones i can remember - and forgive me cus it's been a while since i saw the fim and i've got to admit it's also been a longer while since i looked at the bible.....