SFTS, the OP is right to compare anti-religious feeling to homophobia. On a thread you be anti-religious and you can be homophobic, but in a nursery or a workplace you cannot be.
Discrimination against people on the grounds of sexual orientation and religious belief are illegal, and a nursery could not make negative remarks about religion or sexual orientation.
The whole problem with this thread seems to be that people believe they have the right to decide what state funded institutions can tell their children; they don't (although you can withdraw your child from certain activities).
A state funded nursery has to abide by the law, not by what parents want. If you do not like this, then get the law changed. The protection of religious belief is about equal in law to the protection of sexual orientation; both have less protection than matters of gender, race and disability. The equal standing of sexual orientation/religion has been tested in many court rulings that have arisen from the Equality Act.
Believing in Santa Claus and fairies is not a recognised religion and is not protected by any law.
If you are unsure about anything your child is told by the state, you can phone an equality and diversity worker in the education section of your LEA for advice.
A civil partnership is so called to differentiate it from a marriage. Legally, they have parity, but the names are different because that is what some religious people wanted. We are not a secular state, we have an established church headed by the Queen, and that means Christians do have some power in influencing the making of laws in this country; if you don't like that, fight to change it.