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Cyan comments on The Nature of Offense - Less Wrong
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The Y chromosome is physically much smaller than all the other chromosomes. In particular, it's not an equal partner to the X chromosome. From Wikipedia, I learned that the human Y chromosome contains 86 genes, which code for only 23 distinct proteins.
One example of a sex-linked trait that's wasn't due to selection is colorblindness, which is common only in males because the relevant genes are recessive and located on the X chromosome.
At some point, a population of organisms developed some sex determination genes. Over time, this system developed into the XY sex determination system: sexual dimorphism due to the segregation of sex-determining genetic information onto a single highly degenerate chromosome. I think it's very implausible that this segregation is without evolutionary benefit. The occurence of sex-linked monogenic traits like the example you give here are a side effect whose evolutionary cost was outweighed by the benefit of the development of the XY system. So I don't think this is a good example for the claim you are trying to defend.