The objection is that five individuals, in eccense over turned not only the votes, twice, of millions of Californians, but created a new definition of a significant social institution.
If millions of Californians voted to ban all gun sales in the state, would you agree that the Supreme Court should let their decision stand?
Of course not. There is a Constitutional Amendment that allows for gun ownership.
There is also a Constitutional Amendment that doesn't allow for parts of the Defense of Marriage Act.
Just because millions of people express an opinion at the polls does not mean that they can overturn the Constitution.
The only way to change the Constitution is by way of amendment. There is no amendment barring same-sex marriage.