There is no such thing as homophobia with good intent.
What your mother is displaying is ignorance, not homophobia.
This is partly true. It's ignorant because what she said implies that she thinks that you have control over whether or not you are gay, but her worries are not based upon the fact that you are gay, but based upon the fact that our society is backwards and gay people face discrimination and bigotry.
I am pregnant with a son and I'm not ignorant at all. If my son is gay, I know that he's gay and I can't change that. I wouldn't want to change that, because I'm going to love him no matter who he is and I'll always accept him.
But I still worry about whether his life will be harder, and I don't believe that has anything to do with ignorance or homophobia. That has to do with love and being a mother and growing up in a society that has treated gay people so badly.
I've thought about this a lot and I've thought a lot about how I will feel if my son is gay. My primary concern is that the world won't change enough and that he'll have a hard time, especially when he's young. That concern isn't ignorance, it's based upon fact. Puberty was incredibly difficult for me, and I wasn't a gay boy. Being worried about what sort of heartaches my child may face in life due to his sexual orientation isn't homophobic or ignorant IMO, it's based upon harsh realities of how unfair the world has been to been to gay people. That's not ignorant at all. It's just true.
I don't want my son to experience the things I know that my gay friends have experienced. It's out of my control, since I can't change the world to be a more accepting place, but it's still one of the things that I still worry about it anyway because I already love him.