What makes someone male?

Whether we are male or female is an earthly, physical quality. Our gender is determined by our chromosomes, hormones, and our actual physical bodies - if you have a uterus, that indicates you are female and your chromosomes are XX, not XY.

Jesus lived here on earth as a human being. He could not be genderless. For the time and place he came to, it made much more sense to incarnate as a man than as a woman - if the Word had come to earth as a female, few would have listened to her or taken her seriously. She wouldn't have even been allowed to set foot in the inner courts of the temple. Jesus had a beard (there is a verse that says it was plucked out); there is a verse that says he was circumcised as an infant; those things indicate he was humanly male. But God doesn't have a beard and was not circumcised - God is not a man, God is spirit. I have not seen anything to indicate that a Spirit has a gender.

God is referred to as "Father" and as "he", for OUR sake, to try to help us better imagine and relate to God. God is certainly not an "it", and if I have to use a pronoun for God, I will use "he", but I know that is from traditions and customs of men. It's easier, and not awkward like "Father/Mother God", which IMO, is not really accurate either. But when I pray the Lord's Prayer, I pray, "Our Creator, who art in Heaven..."

The Holy Spirit is referred to in some passages with male pronouns - again, I believe, to illustrate that the Spirit is not an impersonal "it", or just an active force, as some teach, but truly God. But interestingly, the Wisdom of God is clearly identified as female, and many of the early churches equated Wisdom, Sophia, as the Holy Spirit. Also, the Shekinah Glory, the presence of God, is described in feminine terms. It's a divine mystery to be sure, but since both the Father and the Holy Spirit are fully God, and both men AND women are created in the image of God - not just men - I believe that the Father represents what we humans perceive as the "masculine" qualities of God, the "Father" qualities (provider, protector, strength, etc), and the Holy Spirit represents the "feminine" "Mother" qualities (mercy, compassion, comfort, etc). That's just my take on it, my best way of understanding.