Why Does Fox Make Fantastic Four Movies?
Constantin Films and 20th Century Fox spent years developing their big-budget Fantastic Four movie (thanks to an extension by Marvel in 1999) before finally releasing the product, co-produced by Arad and Marvel Enterprises, in 2005, starring Ioan Gruffudd, Jessica Alba, Chris Evans, Michael Chiklis, and Julian McMahon. While we don't know the exact details of Constantin's deal with Fox, the Hollywood studio does possess distribution rights for the characters (similar to Paramount Pictures once controlling distribution for Iron Man, Thor, and The Avengers), via Marvel's 1999 agreement with the studio. Because Fox has co-produced and distributed the only Fantastic Four movies ever to make it onto the big screen, they've been associated with the franchise in the eyes of the general public - but the Fantastic Four's production rights aren't theirs to sell (remember, there are two sets of rights we're talking about here: production and distribution).
Constantin Films' partnership with 20th Century Fox, though confounding to the uninitiated, actually isn't unprecedented. For instance, Warner Bros. Pictures-owned New Line Cinema is responsible for producing each and every installment in Peter Jackson's Middle-Earth series, and they are currently working in-tandem with Amazon Studios to bring J.R.R. Tolkien's Middle-Earth to life on the small screen, but New Line doesn't actually hold the rights to Tolkien's narratives; The Saul Zaentz Company (which operates as Middle-Earth Enterprises) does, and they license out the books' film rights to New Line Cinema. So, for argument's sake, if New Line Cinema were to be bought by, say, Paramount Pictures, the actual rights stay with Middle-Earth Enterprises, but the license would most likely transfer over to Paramount, which would allow them to make more movies if they wanted.
Will the Fantastic Four License Transfer to Disney?
Unlike the aforementioned licensing contract between Middle-Earth Enterprises and New Line Cinema, Constantin Films is an actual production company that produces their films alongside their studio partners. Although Constantin Films' agreement with 20th Century Fox remains unclear at this stage, as the fine print of their arrangement has never been made public, there's always a chance they may be unwilling relinquish creative control of the franchise to Marvel Studios, should the Mouse House move forward with their acquisition of 20th Century Fox (and obtain the distribution rights to the Fantastic Four).
Contractually, Disney buying 20th Century Fox doesn't grant them the film rights to the Fantastic Four, but they could conniving enough to inhibit Constantin Films from making another movie without their say-so. If Disney controls distribution, Constantin would have no choice but to work with the Mouse House (and, by extension, Marvel Studios) on another Fantastic Four movie. Otherwise, they could make a movie without the ability or legal right to distribute it - which would be pointless for the studio and, essentially, make the film another ashcan copy.
These distinct details and clauses aren't available to the public for analyzing, so this is only speculation at this point. We'll just have to wait and see what happens in the end.