Let's not jump to conclusions. Having male privilege doesn't mean you have it to the same extent as others, nor that you keep it after you transition, though some effects (higher confidence in the areas of math, leadership, and basic intelligence, for instance) might stick around. Even if those effects linger for you, it doesn't make you a bad person or less of a woman; it just makes you a
more confident woman. Your wife might as well resent younger generations of women who have benefitted from feminist activism.
Let's also not forget that male privilege is not the only kind of privilege in the world. Being white, able-bodied, American, anglophone, employed, well-educated, middle- or upper-class, young, etc., all give you privilege. Being cisgendered is a biggie. One of the biggest, and one you wife eating up. But speaking for myself, on the social totem pole I'm preciously close to the top.
And Jenny, if you never really lived in a male role, that's a different story. But if you did, even if you didn't want to, people treated you differently as a result, and that guess you privilege, regardless whatever other oppression you might have experienced.