The Queen has often expressed strong support for Christianity and for Jesus in particular. Most people don't mind that she hasn't remained neutral about her religious beliefs.
It's fine for Payette to be openly atheist. There is absolutely no reason for her to hide it.
http://www.patheos.com/blogs/friendlyatheist/2017/06/27/canadians-would-...
The Angus Reid Institute found that an astonishing 80% of the population would have no problem voting for a party led by someone who’s an atheist. (By comparison, Gallup found in 2015 that only 58% of U.S. voters were comfortable supporting an atheist from their own party for President.)
Read more at http://www.patheos.com/blogs/friendlyatheist/2017/06/27/canadians-would-...
I'm not saying we can sit back and relax but atheism is not under threat in Canada.