The variant human's feat represent humanity's larger and more varying natural potential. Other races are better suited towards certain particular things, but humanity has the advantage of diversity -- they are less powerful on average but have a higher variance and potential to excel of individuals. Humans are weaker but better at adapting.
That is why they get hardly any racial features. If anything, giving every race a free feat is what would throw off the "character creation meta" as it would leave humans without any bonuses compared to other races.
That's why, if every other race gets a free feat, Variant Humans start off with 2 feats!
