Marriage is a religious institution. Religion invented it, religious figures perform the ceremony, and religions view it as a way to stabilize their "flock." Somehow, the federal government, which is supposed to be restrained by the 1st amendment: "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof..." created a federal tax code that discriminates against people based on whether they're married and even how many living offspring they produce in or out of wedlock. That, in my humble opinion, is a law that respects an establishment of religion by offering different tax statuses based on participation in a religious institution.
I personally don't give a warm fart what people do in the privacy of their own homes, and I don't think the government should either. The moral issue I see at stake here is equality under the law. Equality for people whether they're married or not, or whether they've procreated or not.
Choosing to create a contract between you and your significant other is not the government's business, and their attempts to alter the behavior of the people with tax policy is despicable.