I stopped thinking about such things as I always got stuck in a head wrenching recursive loop of futility.
As mkrecny stated, choosing to observe and predict the micro aspects of our universe is a lost cause. However, finding patterns in higher levels of systems is what makes science works. While micro systems are usually the areas left for theorists, macro systems have real life applications for scientists. We predict things every day and some things are simply easier to predict than others.
An additional (and perhaps stronger) argument is that Rice's theorem states that you cannot in general predict the behavior of deterministic computation. You can't know if a program will ever access the network card, output a letter "A," halt, etc. even though all of these programs are known to be deterministic.
I don't think anyone is saying that we can create a cellular automata (or any computer) capable of simulating the entire universe. That doesn't mean that the universe can't be modeled as one. You can't simulate an Intel i5 CPU in realtime in Windows 7 running on an Intel i5, but that doesn't mean an i5 isn't deterministic.
As a side node, the potential richness and unpredictability of deterministic computations is a major theme of many works by Rudy Rucker. Any investigation of cellular automata will reveal the unpredictability of deterministic computation, which is essentially the whole point behind cellular automata.