The "God doesn't exist" line is pretty much my line for understanding trans issues too. I can respect that you believe these things, and do so sincerely, and that it has a very profound impact on how you live your life and interact with people, without believing it.
It also, I think, gives a handle on when behaviour tips over into genuine transphobia that might be covered by, e.g., workplace anti-discrimination policies.
Saying "I don't believe in god myself" in the context of a discussion about religion should be fine.
Describing someone's belief in god as being like "having an imaginary friend" or "sky fairies" makes you a bit of an arse (as, conversely, does any attempt to evangelise your work colleagues if you're religious).
Repeatedly saying "Fred believes in sky fairies" completely unprompted, just to get a laugh out of your colleagues in the staff canteen - you should be up on a disciplinary for workplace bullying at that point.