To quote Aristotle, "The natural way of [studying physics] is to start from the things which are more knowable and clear to us and proceed towards those which are more knowable by nature; for the same things are not knowable relatively to us and knowable without qualification."
So we start from the basis of our senses and construct simple models based on those, but there is no reason to assume that is all there is or that the universe is simple for us to understand. The universe does not exist for us - for the vast majority of its existence and in the vast majority of its expanse, humans simply did not exist and that made no difference to the universe as a whole. All that is necessary is that we are capable of comprehending the part of the universe in which we live to such an extent as helps us survive (or else we would not have evolved). Anything beyond that is incidental.
As to why there are so many galaxies, a better question would be "why should there not be?". If the universe is such as to allow one of a type of thing to come into being, it would be reasonable to expect there to be more of that type. Wherever in the universe the causes that led to the formation of our galaxy are present, a galaxy like our own could be expected to form, and the only limitation on this would be if there was insufficient matter to create more than one galaxy. But we have no a priori reason to posit a limitation on the matter in the universe (in fact, if we were to guess at the size of the universe, it would be more reasonable to suggest the universe were infinite rather than of any particular size) and, by observation, we can establish a lower bound on the quantity of matter - that being the amount in the observable universe, which is clearly more than one galaxy's worth. So we know that there must be more than one galaxy and it is entirely possible that there are an infinite number. All of that makes it harder for us to comprehend the scale of the universe, but in no way makes the universe less sensical overall, since when the initial conditions are a particular way and acted upon by the same fundamental principles, the same result will be produced. Thus the goal in science is, through observation and experimentation, to come to an understanding of this process such that we can apply it to particular cases, but not to actually know everything there is to know about every particular thing in the universe. And it is in that way that the universe is comprehensible, whether there is one galaxy or many, as the number of particulars is for the most part irrelevant.
