[I am now thinking that the following line of argument is probably deeply spiritually mistaken. Or, maybe, the issue is this: It is the universe conceived of naturalistically that is small. But the universe that we in fact inhabit lacks that kind of smallness for it images the glory of God. So perhaps there is still an ad hominem against naturalism in the line of thought.]
Suppose I and a few other people were born and lived on the inner surface of a sphere that was a kilometer in diameter. Walk 3.14 km, and you're back where you started. And that was all. As far as I could tell, things had always been in the sphere more or less the same as far back as one could tell, with a small stable population and a simple, self-contained ecosystem. There is nothing particularly mysterious in this ecosystem, and there even is a little library containing books written by my ancestors which give complete systmes of physics, chemistry and biology that fit with all the data.
I think there is an intuition one might have after one had surveyed this meager habitat: there has to be more to reality than this. This intuition could be bolstered by arguments from design or causation, but I think it could also be a self-standing intuition: this can't be all there is.
Now our universe is bigger than that sphere. But I do not think that sheer size is what makes a difference. When I reflect on my stargazing, instead of thinking of the vastness and mystery of the physical world, I have lately been thinking about a certain kind of smallness that it has. Sure, there are untold numbers of stars arranged in untold numbers of galaxies. But even that one kilometer sphere had untold numbers of grains of dust, and that didn't make it all that large. The universe is physically large relative to us, but it exhibits a lawlike unity, and while there are many stars, they can mostly be classified into a limited number of types and subtypes. And this vast universe is, nonetheless, one that is small enough that we can have all-encompassing cosmological theories—that we can hold it all in our mind. It is true that our present theories are not good enough. But we seem to be making progress.
If this is right, then I think it is possible to have a similar kind of smallness intuition about the universe as a whole: this can't be all there is to reality. Reflecting on the universe as a whole—a whole made up of physical parts, indeed largely made up of parts like electrons, neutrinos and/or electromagnetic fields that are pretty familiar to us—can make the universe seem small to the mind's eye. Not small physically, of course. The relevant kind of conceptual smallness is compatible with the universe having infinite spatial extent. Rather, it is small in some deeper sense, despite all its wonder and glory.
I think this may be a way in which the physical universe proclaims to us that it is not all there is, that it is not self-sufficient, that while great and full of splendor, it is, after all, but an image. And unless it is seen expressly as an image, it will pale to us. For a while one might enjoy looking at the calligraphy in a manuscript. But eventually, unless one starts reading what the text says, the manuscript will probably stop being all that interesting. But once seen as pointing to something greater, indeed something infinite (and not just in the uninteresting spatial sense), then it takes on a new, and deeper splendor, one that shines through that natural splendor that was in danger of fading.