It means you’re directing the comment “at” a specific user. It’s a reply-to marker. It started as convention, and Fluther eventually adopted it as an official type thing. If you type ”@”, you’ll get a drop down list of people who’ve previously posted in this thread, for you to select the one you’re replying to.
Note that even when you direct a comment to a specific user via ”@”, it’s still visible to everyone. If you want to send a private message, click on that person’s username.