Why is pH used as a measure of acidity if not only hydronium ions can act as a acid when in solution?
HCl being a strong acid, it is quantitatively dissociated in water, meaning that it fully dissociates into hydronium and chlorides. The hydronium are therefore the main contributors to the acidity of the solution. In a solution of ethanoic acid, the majority of acid molecules are undissociated. This is what "weak acid" means. 

The amount of base necessary to neutralise a given acidic substance can be used as a scale of acid "strength" in chemical risk assessment.