After reading a bit on Wiki, that whole Captain Marvel business is a mess. Fawcett creates Captain Marvel as a ripoff of Superman, and lose the right to publish the character after DC sues them. Meanwhile, Marvel Comics creates a Captain Marvel that is obviously a rip off of Fawcett’s, yet they can get a way with it as long as they publish some sort of Captain Marvel character every couple years or so. DC acquires the rights to Fawcett’s Captain Marvel, but Marvel Comics ninja’d them with their CM, so they have to call him Shazam.
I guess the reason Ms. Marvel is now Captain Marvel is mostly because Marvel Comics just likes using the name a lot.