The issue is that if a charter school receives federal/state funds, they can't really discriminate against children. They can't refuse to take disabled kids. What if they then said, we won't take kids with learning disabilities, or kids who don't speak English well, or kids who are African-American... etc. It becomes a slippery slope. If the tax payers are paying for the school, they do not have the right to discriminate against some kids and refuse them entry into the school.
Children with disabilities are protected by federal laws. They are entitled to receive a public education that places them in the least restrictive environment where they can learn.