The purpose of an amendment is not just to protect rights (although there have been some admendments that have done that, there have been several amendments that are just related to the workings of government, not related to individual rights). You could even find a precedent for an amendment that limited rights in the 18th amendment, which banned liquour and took away the "right" to drink (although limiting "freedoms" would probably be a better term than "rights" since it's not really an innate human right to be able to drink).

Since there is a precent for amendments that don't give rights, or that take them away, there would be a precent for an amendment that would ban homosexual marriage. Whether this amendment is a wise idea is another question. In fairness, very few people (even those who proposed or voted for the amendment) were actually trying to get it passed. It was just a move to get the conservative base fired up and excited, so that they would vote for the congressmen who voted for the amendment.