I’ve fallen prey to this myself: Postmodern Christianity and The Matrix — it’s not what you get out of it so much as what you put into it.
On the other hand, that’s not so different from some people’s treatment of Scripture. The Iglesia ni Cristo interpretation of Isaiah 43:5, for example. But then, that’s outright misinterpretation, rather than the subtle projection of belief which The Matrix induces.
Update: Sparticus lists ways To Abuse The Plot Of Matrix Revolutions To Turn It Into A Christian Allegory.