Fellaini has been linked with a loan move to the Serie A outfit, who claimed a 1-0 pre-season friendly win over Barcelona on Wednesday.
Asked why Javier Mascherano, who was also chased by Napoli, never made the move, Benitez said coaches played no part.
"It didn't depend on the coach but on the project," Benitez said on Wednesday.
"That will be the case with Fellaini too. Van Gaal has nothing to do with it."
Benitez said he was "still missing something" in his squad as Napoli look to close the gap on Serie A giants Juventus and Roma.
Asked if Fellaini was close, Benitez told Sport Mediaset: "Is he? I don't see him.
"When I talk about revenue and wages, I am referring to the ability to construct a strong squad. Our squad is strong but clearly we are still missing something.
"We must continue to form a strong group to recover the lost ground from Juventus and Roma."
