Atheists are more accepting of variations in nature than people that claim to be God's children?
I wouldn't say that. I think it's dependent on the individual and how they assimilate information they've been given. I know about as many so-called 'God's children' who are warm, friendly and very accepting of trans people as those who... aren't. I don't really want to get into the religious angle of it here because that's been mulled over many many times previously. What I would say though, is that there are some
people who refuse to think for themselves, and use a set of rules written down in a very different time in order to judge people based on their own prejudices, using said rules as written authority to justify it. That isn't a reflection on everyone.
All things are shone like beams of light through the prism of one's mind, and split into many colours of differing perceptions through which we see the world.
It does, however, lead me onto what I think about the question in the subject line. I think that those who see something in a negative light, tend to be more forceful in their views and more prominent in their public exposure - maybe because of a subconscious need to get others to share those views in order for them to feel justified. If you accept something, you rarely feel the need to shout about it. It's just sort of a given. You get on with your life and let others get on with theirs. This might tip the balance and give the impression that something is viewed more negatively than it actually is, by virtue of the silent majority staying, well, silent.
If you walk down the street and get abuse by one ignorant butt-barnacle... do you notice that more than the several hundred people you may have walked by who never said a word or even gave you a second glance?