I've worked as a photographer for Scout.com on occasion and I'm good friends with a couple of their analysts (going to a bachelor party for one of them this weekend even though I'm really too old to do so) so I have a little knowledge of how Scout does this...
Usually, school-specific sites are started by individuals that aren't related to Scout. When the site shows enough user traffic, Scout will "lock" them up, so to speak. Typically, it's a renewable contract with the orginal owners still having ownership but becoming Scout employees. A school doesn't have to be FBS to have a Scout website. Scout covers basketball, football, baseball, etc., all the way from high school to the pros. If your site looks like it will make money, then Scout is interested. If your site ends up sucking, they'll look to hook up with a competing site of the same school/team.
Scout also owns many of the sites as well but that's not true of all of them (Dawgman.com, for example).
Make sense?