One of my players has an Ape companion with the Revised Ranger. Do you add the Ape's Strength modifier of +3 to damage rolls as well as the ranger's proficiency bonus?
The relevant passage does not say that you use the proficiency bonus instead of some modifier. Instead, it specifies that you add it:
In addition to the areas where it normally uses its proficiency bonus, an animal companion also adds its proficiency bonus to its AC and to its damage rolls.
The Ape's entry in the MM has a +3 to its damage rolls (probably from its strength, like you say), and the feature does not eliminate that bonus, meaning that it gains +3+(proficiency) to its damage rolls.