The protection of the Great Crested Newt IIRC comes from European legislation. The species is very rare in Europe as a whole, but is commonly found in the UK.
As an example of how common they can be, I was involved with a project where the standard ecology license is for dealing with 100 Great Crested Newts and an application had to be made to exceed it.
The project in question wasn't all that big (only really dealing with a single large farmers field).