You might want a response from Ann or Matt or Angie but to generally clarify a little bit I'm guessing you might be mixing up the Mass. Academy with the institute.

At Xavier's almost everyone is a mutant with few exceptions (the faerie people, a few other creatures with magic instead of actual genetic mutant powers) so there's no secrecy there. The general population of the outside world doesn't know it's an academy for mutants, they think it's just for gifted students so there would be secrecy there but inside the school almost all have powers.

The actual X-men teams on the otherhand are secret. The general student populace doesn't know about the existance of teams so those are kept secret within the school but the mutant powers are common knowledge.

I believe there's a topic in the rules section about the secrecy of the X-men, that might help a little too.

Hope this clarifies things a little!