Children are not “owned” by their mothers either. I know a mother who sold her baby son to a couple of gay men. Was that OK with you?
Bad parents harm their children in many ways, some of them severe, and there isn't any way to prevent. One might make a small dent in the problem by shifting the balance of power from parents to government, but the harm that would do to the children of good parents would far outweigh the small benefit it might afford to the children of bad parents (especially since removing power from parents would reduce the incentives to invest time and effort raising their children optimally, thus likely increasing the number of apathetic parents).
Fundamentally, I regard any ability of government to impose its judgment as superior to that of a child's parents to be dangerous. While it's possible for some small carefully-circumscribed powers to do more good than harm, governments always try to grow their powers beyond their prescribed limits; the more powers governments have, the harder it will keep them from growing out of control. Even if parents were given absolute life and death authority over their own children, the harm bad parents could do to the children of good parents would pale in comparison to what an out of control government will do.
I consider myself a small government libertarian, but unlike many who call themselves libertarians, I recognize that many of the "freedoms" sought by the left are really powers to impose their will on others. Conservatives and libertarians alike both miss the real point of having governments recognize marriages, which is that there are many people who wish to voluntarily bestow courtesies and benefits upon couples meeting certain common criteria, and that having governments recognize marriages which meet those criteria makes it easy for people who wish to bestow courtesies and benefits upon such couples a means of identifying who should receive them. The purpose of the "gay marriage" movement is to restrict the ability of people to choose the beneficiaries of their good will.
One more thing: I would expect that if mothers were allowed to specify whether they wanted to allow their children to be raised by a same-sex couple, or only by a married couple, the vast majority would opt for the latter. I would further expect that “gay rights” advocates would regard this as totally unacceptable, and would complain that such a thing represented “discrimination”. The reason the “gay rights” movement has gone as far as it has is that few people understand what they’re really about. Getting the leaders of that movement on record as saying that a mother who is considering putting her child up for adoption should be forced to give that child to a same-sex couple would help the public realize that the movement isn’t really “pro-freedom” at all.