I don't follow your logic. We have separation of church and state. Having religious symbols displayed by publicly funded schools violates that principle and favors the displayed religion(s). Protecting everyone's right to religious freedom requires not favoring any specific religions. This is pro first amendment.

An LGBT flag is a symbol of support for people who are not cis and straight. It is not a religious symbol. It is not infringing on any individual's right to practice their own religion. This is pro first amendment.

Banning burqas is oppressing muslim students' right to practice their religion, and is anti first amendment.