Morning Waldo,
I'm not sure how old your wee girl is, but I'm guessing she's under 8.
At that age, Bible stories such as 'The Ark, baby Jesus' etc are just that, stories, so she would not understand why you would refuse to have a toy Ark in the house due to your Atheist views and see you as overbearing and unreasonable.
Would you refuse to have her in the house if, she became an adult and able to make an informed decision and said, "Dad, I want to become a member of the local Church and live by Christian values"?