There was an interesting Forbes piece I read last night that answers this question:
https://www.forbes.com/sites/stevensavage/2018/01/04/yes-we-...
TL;DR: because most varieties of bananas in nature are ugly as hell and have seeds; the banana people want must not be like them, and it must also ship efficiently and have good shelf life; only two cultivars managed to hit all of the requirements so far - Gros Michel, and - after it got eaten by disease - Cavendish, which is the one we eat today.
The article points out that the industry has been fully aware of the problems with monoculture for a very long time now, and they don't really have much options to fix it. The text blames modern anti-biotechnology/anti-GMO movements from taking away the one good option we had to solve this - genetic engineering.