Lyric discussion by grid49 

Cover art for All Waters lyrics by Perfume Genius

The song is a wish for a world where he and his boyfriend, Alan Wyffels (who also serves as his main musical collaborator), can hold hands in public without fear, and the lyrics ("When all waters still/ And flowers cover the earth") suggest that it's not going to happen any time soon.

To quote Pitchfork.

My Interpretation

The hesitation is his alone. I see gays holding hands in grocery stores in the south and the 30 or so minutes I am around them (and around dozens if not more people) nobody bothers them. The hesitation is his fear. Society does not accept many things (and with God's teaching on homosexuality, not everything should be accepted), but what stops someone from acting is his own fear...and not necessarily fear of retribution. It could be fear of not being socially accepted by friends; family; co-workers; fear of not measuring up to societal standards; fear of being discovered; etc.

@SweetCheeks2 ....Or fear of people who think that the supreme creator of the universe frowns upon aspects of homosexuality and feel the need to express that opinion.

"God's teaching on homosexuality".... Are you sure no humans were involved?