If you're an academic in the sciences, you have an advantage over your colleagues in the liberal arts: you can write in LaTeX using any editor you choose1. Your document is in plain text and can be operated on by several text processing utilities. If you're an Emacs user, you don't even have to bother with LaTeX; you can write in Org mode and export the result to LaTex for submission. Best of all, you never have to touch Word. Those in the Liberal Arts, on the other hand, almost certainly have to submit their articles in Word format.
Now some of those liberal Arts academics are rebelling and looking for ways to do their writing in plain text too. Of course, they still have to submit their articles in Word format but there are, fortunately, tools that allow this. One such effort is the Scholarly Markdown Project. It's goal is to allow researchers to write in a slightly extended Markdown and use a port of Pandoc to convert it to other formats such as HTML or Word.
The Scholarly Markdown Project is still in the alpha stage so some academics are going their own way. W. Caleb McDaniel is a historian who is using Markdown to produce his books and articles. His post lays out his objection to using Word and then goes on to show how he's replaced it with Markdown. I like how he's not afraid of the Unix tools and uses them to assemble his documents.
We've now reached the stage where anyone who'd rather not use Word has other options but can still submit a final product in Word format. Emacs users have powerful built-in options: they can write in Org-mode and export to
docx format. Those who prefer not to use Emacs, can write in Markdown using any editor they choose and translate to
docx or any other of a number of formats using Pandoc. Lots of people don't mind—or even prefer—Word, of course, and they're free to continue using it. For those who've had enough of that walled garden and all the problems it brings, there are now alternatives.
Yes, yes, a few scientific journals also require submission in Word format but they are, fortunately, few in number.