From the article: “...but this was work Flynn did before he became national security adviser in the White House and was unrelated to the Russia investigation.”
Flynn was working as a lobbyist for a foreign government while working as an adviser to the Trump campaign on national security matters, not as the National Security Adviser in the Trump administration.
I'm not suggesting Flynn's work for Turkey was illegal (let's assume he was properly registered as a foreign lobbyist for the sake of this discussion). I'm suggesting the political optics were awful for Trump.