Letting people have the right to believe in a very old and possibly outdated moralsystem is not overprotecting, its tolerance.
Not letting me criticize them (and introducing legislation for that purpose) is overprotection.
But not letting them have a say in political and scientific decisions is intelligent.
OK, then where do you derive your morality from? Both science and politics need to have some moral axioms. You just make them up with your brain? It's been tried before and it ended quite badly.
With this new knowledge, how can a twothousand year old book (or any religious book, they are all quite old) tell us how to behave today?
You'd be surprised how adequate those old stories still are.
...about being finally able to formulate humanism instead of religion
It's possible to reconcile those two, humanism is not a replacement for religion. As Dostoevsky and Nietzsche perfectly predicted, the process of loosening up of Europe's christian foundations triggered quite a lot of bad events in the 20th century.