Message, shmessage--you're right about that.
The great thing about this film was the filmmaking. Unlike "The Sixth Sense" and "Unbreakable"--both great films--"Signs" was built in the shape of an X. More like a flattened X...><.
Initially, the film is your typical alien invasion flick, with a human-interest subplot. But throughout the film, the place of those two plots are slowly swapped. By the end, the film has become a human-interest film with an alien invasion subplot. The best part is watching the two SLOWLY change places, as the significance of the outside world moves away: first, the television becomes their only point of contact, then that's stripped away and replaced with a radio, until we don't even get real updates from that.
This technique perfectly shows the REAL point of the movie and makes the film something beyond what's been made before: "This is how it's actually going to be when something big and crazy happens. You're not going to be flying your fucking crop duster into the belly of an alien saucer. You're going to be dealing with shit with your family and friends and yourself."
So the finding-his-faith and nothing-is-coincidence messages don't work for some people--big deal. They--and the aliens--are about as essential to the film as the color of the shirt Mel Gibson was wearing in the second scene.