There is an implicit assumption that there is no difference between kids going to traditional schools and the kids going to magnet schools. If there is no difference, then the statistics indeed indicated magnets schools are a poor idea. If, one the other hand, magnet schools get less capable students to begin with then the comparisons don't mean much at all.

A proper test would match comparable students from each type of school at the beginning of the year and then again at the end of the school year. If you can measure the progress made in each group, then you've got something to talk about.