Markdown files can be backed up offline, version controlled with Git, grepped (in-file text search) and finded (search for filenames), parsed with awk perl or sed (yes, sorry, I've done that more often than I like to admit), edited with VIM (I live in VIM), and many other advantages.

In addition to what the other posters mentioned, markdown/plaintext is easier to work with for automation tasks.

For example I schedule tweets through markdown files https://github.com/reidjs/markdown-tweet-scheduler

Twitter doesn't support markdown, though. You're just posting text files. That's only a markdown file by technicality

I sort of misread the post, I meant to respond to why markdown/plaintext instead of Apple Notes or Google Keep. I found it more difficult to automate the task using Apple Notes' sqlite DB than markdown/plaintext files sync'd through iCloud.

For a lot of things such as tables, lists, adding links, etc, markdown allows you to do it "inline" while typing, instead of forcing out of band operations.