Why?
At one time God was wholly responsible for tornadoes, science decided tornadoes would be an interesting thing to look into, so they did. What they found were causes that were natural in origin. For this not to hold you have to make God personally responsible for all those causes.
Too many simplifications in your cosmology there.
The crux of the matter (as touched on earlier by a quote from Russell or Whitehead earlier in the thread) is that you have either an infinite regression of causes, or you go back so far (say the Higgs Boson), or God.
At least those are some of the "popular choices" :-)
The difficulty is that if you allow (even for the sake of argument) the existence of God, and the ability of God to interact with the physical world by whatever means, then it becomes impossible (unless you catch God in the act so to speak) to prove or disprove that God happened to intervene at any one specific point. Because as soon as the event happens, and God "turns his back" on whatever he influenced, the ordinary laws of nature kick in and the subsequent history of whatever God did will become indistinguishable from natural events.
And since God is --for lack of a better word -- "sentinent", (therefore not subject to repeatable mathematical laws which are beloved of physics), the only way to investigate God is not to experiment on Him (even if we know for sure he'd allow it...), but to get to know Him.
And the problem their for the skeptic, the agnostic, the atheist alike, is, all the tools for investigation which perform so dearly when you have known, natural phenomena, suddenly fall to the ground useless.
Hence you have an atheist countering "Pascal's wager" with a counter-dilemna of higher multiplicity: so I go to Hell if I don't believe in God, you say. But I can posit an infinite number of gods, so which one should I believe in...
And it doesn't help the situation that science / empiricism tend to rely on Occam's razor, the null hypothesis, etc.--for the whole ansatz is that it's better to throw away or miss out on things by being too picky, instead of being "taken in" by being too trusting.
But if God is interested personally in human affairs, such trust and willingness to be made a cosmic fool of seem to be required or demanded...
Cheers!