Archbishop John Wester of Santa Fe, New Mexico writes:
The general disposition of the church is one of hospitality, openness and welcome, in the spirit of the new evangelization. Refusing to baptize children of same-sex couples is not in keeping with this outreach, and I find it quite troubling. To refuse baptism to these children solely on the basis of the fact that they have same-sex parents, while possibly done with good intentions, is not supported by church teaching or practice, in my view….
As a pastor, I am also persuaded to baptize children of same-sex parents because the parents, by requesting baptism for their children, are showing good faith. The mere fact that they are approaching the Catholic Church in this regard, knowing that their relationship cannot be recognized as a sacrament, gives evidence that they are serious about their faith and that they wish to raise their children in that faith. Good will on their part should be presumed.
This is a time of grace for the parents. The priest, deacon or lay minister should take advantage of it by spending time with the couple, exploring the faith with them, challenging them to grow in that faith and supporting them in their desire follow Christ as Catholics. I believe that undue attention given to the fact that the couple is gay blinds the church’s minister to the abundance of positive and virtuous qualities that abide in their relationship.
You can read his full article at Outreach.