I think this is a good question, even though it does not lend itself to an easy answer.
In broad terms, it may be easier to answer/quantify as some of the posters have indicated. Things like shape, symmetry or bone structure are fairly simple to pick out as common attributes from a selection of portraits that we agree are 'photogenic.' But I believe that breaks down when we get to the specifics of an individual person.
As far as any individual is concerned, I agree with those who have said it comes from within the person. Whether you call it attitude or honesty, it is an elusive quality that some people just have.
It may instead reflect back on the viewer, and what they consider to be more representative of reality. From my own observations, I consider models to be generally at the upper end of the pretty/beautiful scale - but ultimately uninteresting. When I look at portraits by Shelby Lee Adams, I find the people may be lower on the pretty/beautiful scale, but they look far more interesting to me. (And by interesting, I mean people who have no pretension about who they are, and people that I would like to know.)