I read that it's due to historical reasons, but I wasn't able to find any details. Does anybody know why?
Based on the Czech explanation that we had at school, the Elbe valley was inhabited in a deep prehistory and the Celts considered its as the main river. Vltava, while at its confluence is a bigger and has a higher discharge, meets Elbe at angle and its watershed in the Celtic times was a deeply forested and sparsely populated. Throughout Bohemia, Vltava goes through series of deep gorges and canyons with a few areas that could be crossed. The Vltava valley leaves the gorge just north of Prague where there is a fertile land of lower Vltava vale. Prague was formed on the ford around 870. For inhabitants of ancient Bohemia, lets be Celts, Marcomanni, and Slavs, the main waterway to them was Elbe. The core of the earliest Bohemian Czech tribe was north of Prague in centers like Budec, Melnik, Kourim, and Levy Hradec, which are in a lower Vltava vale and Elbe valley. Therefore, the Elbe was given name to the river and Vltava is a tributary.