First of all, he doesn't do that at every interview. He's probably not done it very much at all. However, many of these "interviews" are from press junkets--a lot like post-game scrum "interviews" with players in pro sports--and multiple media outlets carry the same quotation. This makes it seem far more frequent than it actually is.
Even if it wasn't every interview, he did mention it more times than was necessary. How many times while doing the X-Men movies did Bryan Singer say "I've always been more of a Superman fan than X-Men"? Did he even say that at all while working on X-Men?
Second, since your concern is about fanboys making films, doesn't the logic of your argument suggest Abrams is a strong choice to direct Trek (leading zeroes notwithstanding )?
That's why I said he was the best choice in principal, and yes, by the same coin he's a horrible choice for Star Wars. Hell, even he thought directing Star Wars was a bad idea, but apparentally Disney wants him that bad.
That said, while he is the best choice for Trek in principal, being a non-fan, as a filmmaker and producer I find a lot of his work leave much to be desired.