How does a company you are competing against for revenue not equate to it effecting Fox? Of course it does don't be silly...
That being said they have completely run this franchise into the ground. Idk how they would ever justify making another film.
More people going to theaters is good for both studios (often you'll see that when a big movie opens, there's "spillover" and other films do well because people either can't get into their first choice or change their mind or other family members want to see different films).
More people going to super-hero films is good for both studios.
More people going to see Marvel-based characters is good for both studios.
If there was a good superhero film opening every weekend, I'd go to the movies every weekend (and I don't think I'm alone). It's not like I'm going to say: "I'm not going to see the Batman movie this weekend because I saw the Fantastic Four movie last weekend."
When people go to theaters, they see posters and trailers for upcoming films and it gets them in the mood to see those films. They also get familiar with the theaters so it's a comfortable place and a fun thing to do on a weekend. I believe going to films increases, rather than decreases the interest in going to other, future films.
There's a lot of elasticity in the demand for superhero films. It's not like a car where you buy one and then you're set. People can see multiple superhero films in the same year and even in the same day if they choose to.
If they were really smart, they'd join forces with Marvel like Sony did, but even if they don't, I don't believe a big box-office FF film would take one dime out of Fox's pocket. On the contrary, if Marvel actually did make a huge FF film, I think it would directly increase revenue at Fox. Not just by increasing interest in properties like X-Men, the interest in FF from a big film would generate some interest in previous FF films and likely directly lead to increased sales of Fox FF DVD's and Blu-rays and direct revenue in that form.