Don't think of bench press as a chest exercise. its a full body movement, using chest/back/shoulders/tris/bis/legs... I don't use bench press to build strength and size, I use it to test it. Your shoulders could hurt for various reasons; poor form-using too much delt, elbows flared, too much weight you're handling improperly and too often, poor warm ups, poor shoulder strengthening, poor shoulder pre habilitation.
There's a million different ways to build upper body mass without the bench press.