"Why is there something rather than nothing?" In some ways, it's the most puzzling question of all. Because even if we can explain everything about the universe, (e.g. why there are humans is because of evolution; why there is matter is because of energy) what we cannot explain is why there is anything at all.
There are many problems with such a question, the main one is that we assume that nothing is the natural state of things. We know that there has to be something but how can we assume that it all came from nothing? Some cite the big bang as showing something came from nothing, but any superficial resemblance to the question is a product of the inadequacy of language.
And it's there where a grave concern lies. Our capacity for language is something astounding, evolutionary speaking, there's no animal that even comes close to what we have in terms of communication skills. Yet how could we possibly expect that language to be able to properly comprehend something like the origin of the universe? Perhaps if we can gain a sense of conceptual clarity then the question can be asked in a more meaningful way, but when there are those who take "quantum vacuum fluctuations" are something, or complain that the scientific answer doesn't satisfy the philosophical question, it's reducing the question to a mere word-game*.
*If theists say that something comes from nothing, does that mean God is nothing? Check-mate, theists!