Popularity is not an argument for quality. See: crocs, Justin Bieber, PHP.
Those companies you mentioned, like many others, probably use it because they're locked in that technology, not because it's a superior one. Just like banks still use COBOL.
If you're interested on knowing why using MySQL isn't a good idea, there's this (highly opinionated, obviously) post about it: http://grimoire.ca/mysql/choose-something-else