Closer to a State ReligionLegalizing same sex marriage puts the nation on the road to creating a state religion. You may not have to attend a state church, but you do have to pay for it, and you can't oppose its tenets.
Government support of an issue is not neutral. It is coercive. When actions are codified as "rights" people's ability to argue that they are immoral becomes restricted. In an instant, everybody has to support the values the government has prescribed, and arguing against them brings the risk of fines or imprisonment. Tolerance shouldn't require that I support things I may find morally wrong. Tolerance simply requires that I not persecute people who do those things.
Different IssuesLegalizing same sex marriage inadvertently addresses a more fundamental issue than whether same sex couples should be allowed to live together, love each other or share experiences. With or without legislation they can have legitimate, loving relationships, protected from persecution and violence. Homosexual couples are under the same restrictions and inconveniences as heterosexual couples that do not choose to marry (which is a growing number). The real question that a law on marriage addresses is what standards a relationship must meet in order to enjoy certain societal benefits. This debate is not fundamentally about the legal rights of gays; it is about society's values.
If government has the authority to define those values by defining what marriage fundamentally is, what are its limits in moral issues? If the government is allowed to enforce morals (even if we may support them), it will have precedent to enforce morals we may disagree with later. We cannot risk assigning government to police our values.