You misunderstand the concept of a "protected class."
Employment law indicates that discrimination or harassment based on protected classifications is illegal. A protected classification is something like "gender," but not "being a woman." So if you discriminate against someone because she's a woman, that's illegal because you're discriminating based on a protected class (gender); and if you discriminate against someone because he's a man, that's ALSO illegal because you yet again are discriminating based on a protected class (gender).
Same thing about race, national origin, and a few other classifications (military service, in a few states sexual orientation, etc).
That doesn't mean, however, that you can't have a charity that focuses on one gender or race, or an organization focused on one gender (e.g. girl scouts or boy scouts); it also doesn't mean that an entity seeking to donate money must donate money equally to all genders -- protected classifications are an area in employment law, not every facet of life.