Because they have bad blood with fox or at least Marvel Studios' CEO does..on the comic side, they'll be fine and they'll be back after secret wars, the editor in chief has already stated so. That's something personal between he and Fox, which interferes with business and we all know letting personal feelings interfere with business is in fact, bad business.
And again, I firmly believe the competition is something drummed up with fans at least the idea of it being some heated rivalry; if anything its healthy competition and Kevin Feige has already said he welcomes that because he's a fan of superman and batman and that whole lineup just like the filmmakers who work for him. It's not that serious to them because they believe, unlike many fans apparently, that liking one doesn't mean you'll dislike the other. Me going to see a batman/superman film doesn't mean I won't go see Civil War or vice versa, just like me buying a spider man comic doesn't mean I won't buy a batman comic. Are there people who act like they can only like one company or one group? Yeah of course, but I'd wager with you that it's a very small percentage of fans who are like that while the masses just want to be entertained
