Because there is no crystal ball when scheduling. Schedules are made 5, 10 or even 20 or more years in advance. A team that schedules an FCS team does so with the primary purpose of scheduling a cupcake. A team that schedules an FBS team can't know for sure what that team will be like 5 or more years from when the schedule was created, but they should get credit for trying to schedule a tougher team. A team's intent when scheduling should matter.
Over the last several years we've seen several FCS teams upset some FBS teams. It makes sports headlines. Everyone hears and makes a big deal about it but we shouldn't let those rare occurrences fool us into thinking that FCS teams are tougher than they are. Everyone talks about the occasional upset but no one talks about what happened in all of the other FBS vs. FCS games. As should be expected, those games are usually blowouts. Overall, FCS records against FBS teams is still extremely dismal which is why some FBS teams schedule them. They are trying to pad their resume. When team X scheduled a Georgia Tech 10 years ago, they couldn't have known GT would suck in 2019 and they shouldn't be punished for not knowing.