I am stucked with the following exercise from an elementary set theory course. Any help, even just a small advice on how to start, would be appreciated.
Let $(S,<)$ be a total order and suppose $S$ to be a countable set. If the cardinality of the automorphisms of $(S,<)$ is more than countable, prove that then it is exactly $2^{\aleph_0}$. This is of course without assuming CH.
I edited the orginal post by writing the correct hypothesis, namely $\vert \operatorname{Aut}(S) \vert>\aleph_0$.
The edited post is correct, and is an instance of the "definable continuum hypothesis" theme common in descriptive set theory.
Fixing a bijection between the (underlying set of the) linear order $\mathcal{S}=(S;\le)$ in question and the natural numbers, the set of automorphisms of $\mathcal{S}$ can be reconstrued as a set of points in Baire space $\mathbb{N}^\mathbb{N}$. Being injective and order-preserving are each closed properties, and surjectivity is a $G_\delta$ property, so the set of (sequences corresponding to) automorphisms is $G_\delta$. Now use the fact that every uncountable $G_\delta$ set has size continuum.
In case you haven't proved that fact already, here's the general strategy:
In fact a more advanced analogue of this ("unfolding" - see Kechris, Classical descriptive set theory, chapter II.21.B) applies to arbitrary analytic sets, but that goes a bit far afield.