The parents have a case in my opinion. You're right, they do. Conservatism is closely connected to general patriotism, but it should also be in tune with respecting the rights of the individual.
If Mom and Dad are OK with his not saying the Pledge, then that ends it. I may not like their view, but I respect their right.
Some parents don't want their kids taking sex ed classes. Others don't want them having to say the pledge. Different strokes for different folks. In any case, being forced in a public school to do something that severely violates one's religious or political beliefs is wrong.