If you are a Protestant who has ever attended a Catholic Church then you have probably noticed the parishioners executed a strange sort of bow. Before entering the pew, your Catholic friend probably dropped to his/her right knee while crossing themselves. I promise you, this is not done with the intent of tripping the poor, unsuspecting Protestant visitor so that we can silently laugh. LOL
The practice appears to have started during the Middle Ages when it was common to genuflect to people in positions of power. Gradually the practice entered the Church where it has remained as a form of devotion and respect to Christ
When most Protestants say that God is present in their church they normally are speaking about the presence of Holy Spirit. Because I believe my nonCatholic friends when they tell me that they are Christian, I don't doubt that they experience grace in their lives and churches.
But when Catholics-and some Lutherans and Methodists- say that God is present in our Church we mean that Christ, through the Eucharist, is actually physically present in our mass. Under the guise of bread and wine, we get the opportunity to literally touch our Lord. When we bend our knee, we are expressing our reverence. Being in the physical presence of Jesus Christ is an honor. Genuflection is an act of humility. Catholics take seriously the verse that states that 'Every knee shall bow."
I should add that most most of my experiences with nonCatholic Churches have been with evangelicals. So, if your particular Protestant Church has practices that are similar to Catholics, I apologize for being overly general in my description of Protestant practices.