Today my wife told me apologetically that she asked our three month old boy to pray for me. How should I react?

Anger, because we have this solemn agreement between us that our son will grow up without any religious affiliation and will be free to choose his path when he turns 18? And prayer is a part of religion, all of them (and especially hers) and by teaching him to pray she is teaching him a fundamental religious concept. One which has been proven to be completely ineffective and thus untrue.

Gratitude, to learn that she cares about me so much and wishes for my well-being so strongly to direct her best weapon to my side in my times of trouble and/or difficulties and make it doubly effective by involving our infant son in the exercise?

Or fear that our son may have his vision always clouded by these delusions and never see the truth due to being constantly bombarded by religion from all well-meaning quarters except this one?

Son, if I did believe in prayer and could pray, I would pray that your eyes always be open, your mind always be free and that your heart always be big. The rest is a given.