Any metric can be exploited and the MCU just so happens to break that system. Yeah, no MCU film has a rotten score, including Iron Man 2 and Thor 2...These are indefensibly bad films.
Yes, the RT system overwhelmingly favours MCU films, really for variety of reasons, but the most predominate among them is the shared universe factor. If you watch Red Letter Media's review of Captain Marvel, Rich says that Captain Marvel is a mediocre film and does not recommend it, but Mike says you should because it's part of the MCU. This has actually been a trend for reviewing these films since the very beginning, with some reviewers noting the post-credits scene in Incredible Hulk as the most interesting part of the film.
MCU films do get extra 'points' for simply being part of that shared universe and since the you simply have to 'like' a movie to give it a positive score on RT, that's really all you need.