Yes, I didn't disagree with that. What I disagree with is that beginning of time means god exists.

As long as the net gain or loss is zero, energy is conserved. Anyway, calling the idea that the universe itself is one of these quantum fluctuations a theory was perhaps a bit generous; it'd be more accurate to call it speculation, since there's no evidence for it. But it doesn't break any laws of physics.
It does if you have no energy.

alright, I'll try again. Virtual particles don't exist on their own, they are a result of a quantum reaction. It's not particles coming from nothing, they're coming from energy (photons). It's energy turning into matter, not nothing turning into matter. It's called 'pair production'.
Exactly, energy allows them to form.

Yes, I didn't disagree with that. What I disagree with is that beginning of time means god exists.
1. Matter, time, energy and space had a beginning. (this is the one Hawking showed)
2. Everything that has a beginning must be caused by something else (possibly plural).
Derived Premises
3. Matter, time, energy and space was caused by something.
Conclusion
Something (can be plural) existed before time began and caused the beginning of matter, time, space and energy, we call this being God. (or these beings Gods)

1. Conclusion from above
Now we have two possibilities.
2a. The "God" or "Gods" from above was caused by something else.
or
2b. The "God" or "Gods" from above was not caused by something else.
if 2b, then that will be our premise.
otherwise replace "God" or "Gods" with the being(s) that caused it.
eventually we will have a premise similar to 2b. (Rename the thing(s) that was not created God(s))
3. Everything that has a beginning must be caused by something else (possibly plural).
Derived Premise
4. "God" or "Gods" did not have a beginning.
Conclusion
"God" or "Gods" exists and did not have a beginning.
This may need some fine tuning, but it is pretty close.

As Doomgaze said, this could just imply a far superior race to ours, that exists in a universe that does not obey our rules, but all the evidence points to being(s) which have godlike powers.