Is it known exactly why the tomb where Henry VIII and Jane Seymour were buried was deemed a good resting place for Charles I as well? I see no connection between the three that would lead me to believe there was a good reason why he was buried with them.
Perhaps it was thought that Charles I deserved to be buried with another King viewed as a tyrant or perhaps it was just easy to get into that vault and bury him there. I don't know. You can read more about it at http://www.stgeorges-windsor.org/assets/files/LearningResources/BackgroundNotesHenryVIII.pdf