Biology plays an important role in society. For example, take a husband and wife who conceive a child with the help of a sperm bank. It is unlikely anyone will ever ask that couple, "Who is the 'real' father?" If they were to divorce, the husband, even though he is not biologically related to the child, should be in a good position for all of the rights he would get as a biological father.
This is not always so with same-sex couples. While it is true that the legal right to marry has secured a good deal of peace of mind for some of these couples, the reality is that biology remains the basis for some parts of the law or judges' decisions.
Reliant on the other parent's goodwill
Many same-sex couples make the decision together to have a child. Sometimes, they jointly adopt a child, and by both becoming the child's legal parents, they have protections. An issue arises when one person in the couple is the biological parent, such as when a woman gets pregnant and bears her biological child. If she were married to a man and used donor sperm from a bank, there would likely be no problem down the road if they split up. On the other hand, a nonbiological or nongestational same-sex parent should adopt the child to cover all bases. Otherwise, in the eventuality of a split, whether the parent gets some form of custody could possibly come down to the other parent's goodwill.
Law catching up
The good news is that such cases of same-sex parents not being able to see their children should be on the decrease. The legal system now is more about considering the best interests of the child rather than relying on treating legal principles as black-and-white issues. So, if you feel hopeless about your chances of seeing your child again based on stories you heard from 10 years ago or even five years ago, know that the landscape has changed dramatically.