Indeed Marc.
Universal own the rights to use the characters of Marvel comics within Islands of Adventure as per the agreement they would have made with Marvel back in the 90s when the park began. This does not give them any rights over the characters as such. Just the ability to use them within IoA. Either way, they would have paid Marvel for this deal and the use of it's copywritten material. Essentially, like a song, the characters have a royalty system. Since Universal would have paid Marvel for this, it is safe to assume that as Disney now owns Marvel, the money paid for the exclusive rights for use of the Characters within its park would be now paid to Disney. Unless of course Marvel were allowing the use of the characters within IoA free of charge, which I would find most unusual.
It is similar with the exact reason why JK Rowling refused to sell the character of Harry Potter to Warner Bros. Had she sold the characters themselves WB could do with it whatever they see fit. By her only selling the rights to the stories they are unable to do anything outside of the set stories with Harry Potter. However, they can represent the stories (within certain contractual obligations) however they like and she would be paid accordingly for the use of her stories and characters.
Marvel would never have signed over the characters to Universal as ownership, only the ability to use them. A privelage Universal would be paying for.
Subsequently, Iger (from Disney) has made the statement that any previous arrangements between Marvel and the theme park industry will be honoured. Suggesting that both Marvel and Universal had an arrangement of course and that Disney would take on this arrangement. Hence the thinking that Disney will earn at least some money from the use of the Marvel characters within IoA.