I was raised as a fundamentalist Christian. I don't know the reasoning in Catholicism, but was told to kneel in church as a show of humility and submission to God. I was also told that this was reserved only for God.

I'm no longer religious. I couldn't tolerate the bigotry towards gay people. But the idea of kneeling for a human being repulses me.

If the act of kneeing at all is a problem for you, then I don’t know what to tell you. But kneeling to others, and kneeling with others—joining in with others who are kneeling—are very different actions. I’d suggest you not conflating the two.