The usual way this argument runs is that atheism relies on certainty about the origins of the universe - i.e. the proposition that there definitely was no creator. So, if we don't yet fully understand why anything exists, what basis do atheists have (other than faith) to believe that there was no creator?
I confess that this argument stopped me in my tracks for a while when I saw it made by Peter Hitchens, and for some time caused me to consider myself agnostic. But it just didn't settle right with me, and I think there are a few reasons.
1) The idea that there is a creator is not just an idea about the origins of the universe, it's also about the present. Does the universe (as far as we can see) look like it was designed? I find it very difficult to think so, so on its own that makes it impossible for me to really believe in a creator. I also think it's very telling that to believe in a creator one needs to go through a seriously elaborate series of intellectual acrobatics to force it to be compatible with the universe as we know it.
2) I fundamentally do not understand how "faith" or "belief" even comes into questions like the origins of the universe. Theists often accuse atheists of not truly understanding what belief is, and perhaps they are right. But their use of it seems to just step in whenever science doesn't have the answers. So, for a theist, if the origins of the universe remains unknown, the answer to that question becomes one about faith. But how can that be the case? For me, belief seems like an important response to questions that are fundamentally not scientific - how to live, how to be a good person, how to explain beauty, how to tell a good story. "How did the universe come into existence?" is a scientific question specifically about the natural world. If there's no scientific answer then... there just isn't one. I don't understand why faith even comes into it. This usually provokes laughter and scorn for "not understanding faith", but I just don't see how they connect.