I think that's the point. Often Christians (myself included) sense God has spoken through things that could be dismissed as coincidence, but that we know, deep in our bones, isn't. But it is personal and requires faith to believe (and we often only see the benefits in retrospect). I actually think Shyamalan made a decent fist of trying to get this across, without resorting to making God an unambiguous presence in the film.

I rather like Signs, for all its faults. The water thing is ridiculous though. I recently heard someone try to explain it away as a "holy water" metaphor. Still not convinced.