In the Design Guidelines for Developing Class Libraries, Microsoft say:
Do not assign instances of mutable types to read-only fields.
I agree with you completely, and I do sometimes use readonly in my code for mutable reference types.
As an example: I might have some private or protected member -- say, a List -- which I use within a class's methods in all its mutable glory (calling Add, Remove, etc.). I may simply want to put a safeguard in place to ensure that, no matter what, I am always dealing with the same object. This protects both me and other developers from doing something stupid: namely, assigning the member to a new object.
To me, this is often a preferable alternative to using a property with a private set method. Why? Because readonly means the value cannot be changed after instantiation, even by the base class.
In other words, if I had this:
protected List InternalList { get; private set; }
Then I could still set InternalList = new List at any arbitrary point in code in my base class. (This would require a very foolish error on my part, yes; but it would still be possible.)
On the other hand, this:
protected readonly List _internalList;
Makes it unmistakably clear that _internalList can only ever refer to one particular object (the one to which _internalList is set in the constructor).
So I am on your side. The idea that one should refrain from using readonly on a mutable reference type is frustrating to me personally, as it basically presupposes a misunderstanding of the readonly keyword.