While he's worked extensively with superheroes in the past, his cynical, "real-world" take on them tends to give people the impression that he's more Frank Miller than Stan Lee, and the degree to which he's able to play these characters "straight" is certainly a question in the minds of some fans upon reading the news.
Rumor has it that, like Marvel Studios, both Sony (who own the Spider-Man and Ghost Rider franchises) and Fox hope to assemble Marvel Cinematic Universes wherein their characters can interact with one another. That's a fine enough idea, particularly as long as it's a bit more limited than Marvel's and doesn't spin off a team-up film every year from a different corner of the Marvel Comics catalog.
In that capacity, the appeal of using Millar is clearly evident. He's had some success managing smaller crossovers between his own stories, and merging separate-but-related comics plots into a singular film in the form of Kick-Ass 2: Balls to the Wall, which adapts not only the miniseries by the same name, but Hit-Girl as well.
However, any appeal that his work history and skillset bring to "merging a couple of masked adventurer movies," that same history would pretty clearly demonstrate that something as bright and Silver Age-y as The Fantastic Four is way outside of Millar's wheel house. One of the things that works best for those characters is a sense of wonder which is not only absent, but cynically mocked in much of Millar's work.
Can he do a good FF story? It's difficult to say, but it's equally difficult to imagine what one would look like...and if they're using recent history as a guide, it's concerning to wonder how grim and gritty Fox might be hoping to make Josh Trank's Fantastic Four.