Speaking as someone who has done that until I saw someone say something in their journal about how irritated they were by it...
I understand the frustration but not everyone is super savvy with LJ. When I did this - commented on a fic posted in a comm that linked to a personal journal - I assumed that the person posting in *in the community* wanted comments IN THE COMMUNITY. I wasn't on their friends list and while it was publically posted, I assumed that the poster would prefer knowing that the comment came from the community and wasn't some random viewer.
Honestly at the time, I was annoyed that the writer was publically annoyed that people were commenting in the comm and not at the fic journal they had put the fic up at.