The problem with Wordpress is that it takes a long time to really understand, and an continuous effort to keep the website safe and up-to-date.
This is not a problem for big NGOs, but especially the small non-profits usually don't have someone skilled to set up, secure and run a wordpress site.

Not to mention someone who designs their theme. And just buying a theme isn't so easy either, as most themes these days are bloated and slow.

As much as I love wordpress, I feel it's not a good choice for non-profit per-se and other CMS - like Grav - are better, as they are more simple and require less effort to run and secure.