The thesis is in the title - that public schools are shortchanging boys. The author believes that public schools, teachers in particular, expect boys to act like girls in the classroom. The nature of boys is not to sit still, to ask challenging questions, to make teachers prove their points. They are more aggressive in their inquisitiveness.
It is my opinion that the essay is supported by anectodal evidence, that is, the writer's experience. She does give a few facts - i.e. that "only 65 percent of boys earned high school diplomas in the class of 2003, compared with 72 percent of girls." She also points out that girls get better grades, but offers no proof of this statement. There is probably a lot more proof for her thesis available, but she doesn't give very much of it - just stories.
Had I written this essay, I would have added a lot more data to support my thesis. That said, it is not that I do not agree with what she is saying, it's just that more statistics would give more credence to her thoughts.
There is a lot of good research available to support the idea that same-gender classrooms result in better grades and a better education for boys AND girls. I would like to have seen more facts in the essay.