However, when you say this phrase to a person because you feel that they have a fundamental flaw about them, the phrase becomes one of the most hurtful things you could ever say to another person. If you believe God designed people and knew them before they were even born, why do you feel that God made a mistake in making them gay? It is an absolutely despicable attitude. It's analogous to a white person telling a black person that he'll pray for him because he is not white. The phrase, in this way, becomes "I will pray for my idea of you." When you pray that someone will change an inherent quality about them, you have ceased to care about who they actually are. You only care about who you think they should be.
This is multiplied when placed in a family setting. When you write to your family member and say "I will pray for you" because he or she is gay you have ceased caring for who they actually are. You do not love the person they are. You despise it. You only love your own idea of them and what they "should" be in your eyes. It is like a parent who raises a child to become what he or she could not as a child. That parent then judges that child's success along the lines of what success they achieve. There is no actual way to meet the parent's approval because the bar is set too high. It is like attempting to reach the outside of a circle when all you can do is take a step halfway to the outside every time. When you create an idol of what you think a person should be, you cease to love that person and only love the idol because the idol is more fulfilling.
So the question is put into your relationships with those around you: Who do you love? The person as they are, or the idol as you wish them to be?