The nature of the issue of homosexuality is very different from racial segragation. A persons race, for one, is something entirely beyond their control, and therefore not an issue of morality. Secondly, the laws which desegragated schools were designed to prohibit actions against black students, not white supremists right to think what they want. What the civil rights movement wanted was the right for black children to attend school without fear of violence or mistreatment.
The children of homosexuals already posess this right and courts are prepared to protect them from those who would act against this right. This is not enough for some in the pro-gay movement. They want to use the public school system, as you say, to promote their moral agenda over other people’s. They are not satisfied with the legal right to engage in this disordered behavoir. They want to silence all voices which disagree with them by law. They want their beliefs to be taught to all students in public schools.
This is unacceptable. Keep in mind that the few white-supremists that are still active out there still posess the right to speak their opinion, no matter how much we disagree with them. Children in public schools have a right to their religious beliefs and not to have the moral codes of others forced upon them.