1. Paying for parking is a way to weed out a few drivers. The high school doesn't have a lot of extra land on its site and is doesn't have anywhere to expand the parking lot to. If you make parking free everyone will want to drive and there will be no way that the current parking lot will be able to handle the increased parking load.
2. Parking permits are a form of revenue for the school. If the district didn't charge you to park there they would have to come up with that money from somewhere else. The school board and general community are very apprehensive of additional taxes. In particular in light of recent funding choices (diversity coordinator) of the district. People simply don't want to pay additional taxes for an already very well funded school district.