I believe that it depends on the US state, unfortunately. Some issue an "amended birth certificate" with the new information and either seal or at least don't immediately offer the original; some mean it'll be noted in some way ON the form, so that anyone who sees your BC will see that the sex designation has been changed. (And obviously in that case they can likely guess what it used to read, since I don't think any state offers more than two choices for sex marker.)
http://www.lambdalegal.org/publications/sources-of-authority-to-amendSome examples :
Alaska issues a new BC where "Amended birth certificates will note that the sex designation has been changed."
California offers a re-issued certificate with no previous information *if requested by a judge.*
Connecticut automatically offers a re-issued certificate with no indication it was amended.
If you were born in a state where the amended BC would out you, your best bet might be to apply for a US passport - so you do have to show your BC to the passport office, but they won't be as big a deal as, say, an employer or college - and a state driver's license. Generally speaking, once you have those two forms of ID, no one will ask you see your BC anymore (because they are both considered primary forms of ID, and you will be presumed to have shown it as proof of citizenship to get the passport).