There is as of yet insufficient data to produce a meaningful answer.
I would certainly love to tell you that the universe is charge-neutral, because that would imply I know enough about the Universe to say that the number of negative charges exactly equals the number of positive charges in magnitude. Unfortunately, I'm not sure we're able to say that it is perfectly charge neutral. There could be a spare proton, or even a few spare quindecillion protons, somewhere out there imbalancing the Universe's net electric charge, and it would be basically impossible to tell from here. Obviously no such things exist nearby, but we can't rule it out for the entire Universe at large. Heck, we aren't even sure about the large-scale shape of the Universe (probably flat and expanding per FLRW, but we haven't gone to the corners and edges to check). Trying to say that it is charge-neutral would be shocking without further knowledge about what the Big Bang was like.
Of course, the best reason we have for why the Universe might be charge-neutral (if it is, which is strongly believed but again can't be proven really) is because the past timelike singularity of the Big Bang was also charge-neutral. When quarks and leptons W and Z bosons appeared (the only known charged particles), they should have appeared in roughly-equal quantities of particles and antiparticles, which would balance each other out electromagnetically. Again, that raises the question: where's the antimatter? If all kinds of particles were produced in even amounts, there should be more negative charge than positive charge, since up-type quarks have $Q=+2/3$ and down-type quarks have $Q=-1/3$ and leptons have $Q=-1$ (disregarding charged W bosons, which are ephemeral), leading to an overall charge per-set-of-particle of $-2/3$. Antimatter production during the Big Bang would rectify this, but we observe very little antimatter in the Universe compared to matter.
Ultimately, it comes down to "we don't know that it even is charge-neutral, and if it is, we're not sure exactly why". One can say that a charged Universe would not be able to form complex life and hence humans, but that's the boring anthropic answer that beats any question about why the Universe is the way it is. Yes, the Universe probably is charge-neutral from observations, but if it is, the antimatter imbalance problem would be key to understanding why.
If you're willing to accept a charge-conservation answer after all my blabbering, you can just say that the Big Bang singularity was perfectly neutral, and when it generated all the different particles, it could only do so in neutral combinations, leading to a charge-neutral Universe. Whether this includes a backwards-in-time antimass Universe is still up for debate.