You can just read their explanation: https://letsencrypt.org/2015/11/09/why-90-days
Tl;dr is to limit damage from leaked certs and to encourage automation.
Related recently:
Decreasing Certificate Lifetimes to 45 Days
https://news.ycombinator.com/item?id=46117126
Related recently:
Decreasing Certificate Lifetimes to 45 Days
https://news.ycombinator.com/item?id=46117126