Let's start with the initial hierarchy, including F, but before we've declared that F is equivalent to the intersection of A and B:
Then we add (A and B) as a class equivalent to F. Protégé is smart enough to render things that are equivalent or subclasses of intersections under each of the intersected classes, so we see F appear in two places here.
A reasoner can confirm the relation, too. Here I've turned on Pellet, entered F into the DL query, and asked for subclasses. Sure enough, C is a subclass of F:
Here's the ontology that you can copy and paste:
@prefix : <http://stackoverflow.com/q/22221549/1281433/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
:ontology a owl:Ontology .
:A a owl:Class .
:B a owl:Class .
:C a owl:Class ; rdfs:subClassOf :A , :B .
:D a owl:Class ; rdfs:subClassOf :A .
:E a owl:Class ; rdfs:subClassOf :B .
:F a owl:Class ;
owl:equivalentClass [ a owl:Class ;
owl:intersectionOf ( :A :B ) ] .