People say inheritance breaks encapsulation, which i agree with. They say delegation is better- although the modifiers in delegation can also be public/protected.
So is the real reason why inheritance breaks encapsulation because of the "knock-on" effect of the public/protected modifiers from the super class being exposed to any new classes which extend the current subclass?
Yes. Since it gives the derived class access to members of the base class (depending on what language and which kind of inheritance) it is said that it breaks encapsulation. IMHO this is only if you are clinging to encapsulation in the strictest terms. IMHO it is reasonable to say that you are accepting the derived class as an extension of the base and therefore related in some way and not really breaking the encapsulation. Purists will disagree with this.
Take a look at http://www.ccs.neu.edu/research/demeter/papers/context-journal/node17.html and search for "breaks" for an academic explanation.