I think it has more to do with the panicky disavowal of Trek fans. JJ's fall back to "this film is not made for Star Trek fans." This line does not refer to a narrow demographic of fans, but rather "fans."
Holy out-of-context, Batman.
You missed a word in your quote: "necessarily",
as in "The whole point was to try to make this movie for fans of movies, not fans of 'Star Trek,' necessarily".
Here is the entire context of what he said about making the first film for more than just Star Trek fans:
Improving Star Trek means appealing to more than just the devoted Star Trek fan. "The whole point was to try to make this movie for fans of movies, not fans of 'Star Trek,' necessarily," said Abrams. "If you're a fan, we've got one of the writers who's a devout Trekker, so we were able to make sure we were serving the people who are completely enamored with 'Star Trek.' But we are not making the movie for that contingent alone."
I don't think you necessarily deliberately (overtly) left out that word, but I think in your mind, you so badly want Abrams to be this villain who has an agenda to stomp on 45 years of trek history that you actually think he said "this film is not made for Star Trek fans."
Actually, I was thinking of another quotation from the New JJ Abrams interview thread:
"This movie was not made for 'Star Trek' fans; it was made for movie fans."
He does go on to say
"But if you're a 'Star Trek' fan, I think you'll be really happy"
but this is yet another instance of ghettoizing traditional fans. The prioritization is clear. The film is not
made for Star Trek fans, but "movie fans," however, even though the film is not targeted at Star Trek fans, they should like it too.
I wonder what it would be like for a James Bond film to be billed as not made for James Bond fans or if Serenity were billed as not for Firefly fans or if a Star Wars films was billed as "not for Star Wars fans."
He is kinder in the citation you mention, but once again it is a rhetorical distinction separating us from them and assuring the casual theater goer that it is made for them.