This is either a bug… or a feature request. Atom doesn’t have a way to remember syntax highlighting, if you are forcing a certain type of highlighting for something non-standard.
Here’s my use-case: I use Emblem.js and the Ruby Slim package for syntax highlighting. Every time I open up a *.emblem file, Atom refers to it as plain text. There is no way to tell Atom to highlight all files with this extension with the Ruby Slim package, nor does Atom remember my preference.
Slightly annoying. I’ve switched from Sublime 3 beta, which has the option and a bug where it just doesn’t remember. So I’m used to constantly changing my syntax highlighting… But a boy can dream of one day not ever having to always choose how to colorize a file whenever it’s opened!