Gay marriage not an issue of equality
Folks seeking to nix a law on equal protection grounds who belong to non-suspect classifications can still succeed if they can prove that there is no rational basis for the government's position. Gays will be unable to do that.
Why not?
Inequivalence between marriage and race
When a law purportedly discriminates based on a non-protected class (such as were blacks before the Civil Rights movement), anyone trying to challenge government action on equal protection grounds has the burden of demonstrating that the law is discriminatory, and that there is no rational basis for the law's discriminatory purpose or effect. In other words, the gay community has the burden to prove they are being discriminated against. Contrast that with suspect classifications: if someone challenges a government action on the ground that it discriminates on the basis of a suspect classification, the government has the burden of demonstrating that the law has some compelling justification. The government had no justification in segregating blacks from whites, because the burden couldnt be produced; blacks, by there very nature, do not differ one iota from whites, with exception to darker skin (Blacks are offended that they have been compared to gays against their will and without their approval). For this reason, the government may freely discriminate until a gay person can explain how the government is wrong in doing so.
Marriage as a public display
Marriage is more than the solemnization of private relationship: it is the public recognition of the relationship. Thus, gay marriage cannot be thought of as a private issue, covered under privacy laws (such as Roe v. Wade, for example).
Efforts needed to protect marriage
You are not allowed to marry: a relative, the family dog, someone who is already married, someone who is underage, a member of the same gender. The gov't is far less interested in the goings-on behind the scenes, and far more interested protecting the institution of marriage from assault by bigamists, homosexuals, and the family dog.
There are only so many rights that are considered fundamental. These rights deserve very strict protection. Other "rights" do not deserve any Constitutional protection, and therefore laws may be written that undermine those rights if there is a rational basis for doing so.
Gay marriage cant be compared to segregation of the blacks because gender-orientation is not a suspect classification. Race is a suspect classification.