There are really only three reasonable ways for the universe to have come into existence. First, the entirety of our universe is simply an illusion. This belief is held by Hindus and other various religious beliefs. The problem with this outlook is that quite simply, no one really adheres to it. Otherwise, there would be no need for crosswalks or other safety precautions, because what would it really matter? Death and life are only illusions. While this sounds great in the white towers of academia, it is really impractical and inapplicable in real life.
A second option is that the universe is eternal, which is the belief commonly seen in Greek philosophy, as well as other scientists such as Carl Sagan. This is just ridiculous when one considers that we have a finite supply of energy and matter in the current universe. Therefore, it serves to reason that there was no time when we actually had infinite resources. Therefore, if this were the case, the laws of Thermodynamics basically assert that an eternal universe would have died out from heat loss an eternity ago.
Finally, there is the third option that the universe was created. This option is really the only reasonable option. The question then becomes this: who did it? Many scientists contend that it was entirely an operation of impersonal and non-sentient forces that shaped our universe, and that God is an impossibility. In fact, Richard Dawkins echoes your exact same doubt, because he likes to say “Well, who made God?” Scientists have come up with a myriad of explanations to give us an entirely naturalistic way for the universe to come into existence, including the fields of quantum physics and string theory. No explanation given to date has adequately addressed the problem of origins of our universe, because they cannot give an account for how everything happened. Without an explanation, we are left with the impossibility that the universe came about simply from nothing.
You argue very correctly that nothing comes from nothing. However, you are missing the philosophical issues in this argument. Namely, you are denying the possibility of one impossibility in favor of another. Deny the existence of God, and you are left with the impossibility of something giving rise from nothing. What you really need to realize is this: While anything that BEGINS to exist requires a cause, something that is eternal needs no cause. In addition, an effect requires a cause, usually larger than itself. Therefore, when considering these two things, it is only reasonable to believe that the finite universe had an infinite creator that never begin to exist because He already existed.
Another thing to consider is this. The two most reasonable explanations for everything are either an eternal universe or an eternal creator. With our scientific evidence, the first one is impossible. The second one is the only option.
We will not understand everything in this existence. “For now we see indistinctly, as in a mirror, but then face to face,” (1 Corinthians 13:12). We have to be willing to accept that we will not know everything this side of eternity, but we can rest assured knowing that God is going to eventually reveal all to us, and we will know just as we are known.