It's about control. Like most companies Apple prefers not to be dependent on unilateral decisions made by other companies. Even though WebM is free it is controlled by Google. WebM has only one implementation and Google sets the direction of the project. H.264 is the result of cooperation of many companies and has multiple independent implementations. For a huge company like Apple the license fees of H.264 are not important.
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It's about control. Like most companies Apple prefers not to be dependent on unilateral decisions made by other companies. Even though WebM is free it is controlled by Google. WebM has only one implementation and Google sets the direction of the project. H.264 is the result of cooperation of many companies and has multiple independent implementations. For a huge company like Apple the license fees of H.264 are not important.