Domestic Travel... Expensive?!

Since this summer vacation has started and I’ve been planning trips around Japan, I’ve discovered that domestic travel in Japan is expensive. Even though the train system is extremely established, even though there are multiple bus companies patrolling the streets and running buses regularly, it’s still expensive to get anywhere far on publis transportation (that’s including planes). Why? In some ways, it’s cheaper to book a flight to Hong Kong or even Korea than it is to travel to Kyōto.