In this world, theism involving the proven gods would map approximately to atheism in our world. Using this comparison, there are a couple of ways to proceed:
"Yes, but where did those gods come from? Did someone create them?"
This is cool, because you actually have precedent. Someone created this universe. We know that for a fact, and we know who it was. Who's to say this didn't happen recursively? After all, humans created The Sims.
"The so-called 'Gods' are nothing but liars. Here's what really happened..."
We already have people saying scientists are making up lies for the money (what money? I dunno). What's to stop this happening here?
Or further along those lines:
"There are no gods! It's all a plot by Big Theology!"
Not sure if conspiracy theories count as religion, but they can surely be taken to those levels.
"I worship Thor only. Really, all the evidence says he created the universe by himself. The others just pressured him to say otherwise."
We have a variety of religions on Earth that came from the same origin. Why can't that happen here? In addition, they'd likely be treated the same way we treat celebrities; with limited information and blind cherry-picking.
"The gods are not worthy of worship. Nature/enlightenment/the Sun/something else is!"
Not all religions focus on gods in the first place. They would still exist.
"Who? I haven't heard of them."
Maybe they lived in a third world country or one with tightly controlled information. Maybe they're a hermit or live in a tribe separated from the rest of humanity. For whatever reason, they simply haven't heard yet, and they have their own guessed answers to life, the universe, and everything.
I'm sure there are other ways to take this, but mostly it comes down to people not believing what they're told, no matter how scientifically accurate. This would be as true of that world as much as it's true in this.