Rubber Soul is my favourite Beatles album, and Revolver comes next. Maybe Rubber Soul "fillers" ("What Goes On", "Wait", "Run For Your Life") are weaker than the weaker tracks from Revolver ("And Your Bird Can Sing", "Doctor Robert", "I Want To Tell You"); but the most well known songs from Rubber Soul are truly classics ("Norwegian Wood", "Nowhere Man", "Michelle", "In My Life") while few songs from Revolver are as memorable ("Eleanor Rigby" being the great exception). I think that Revolver as a whole is a more consistent album, but Rubber Soul has better individual songs. And this is said by someone whose favourite song of all time is "Tomorrow Never Knows".
About Rubber Soul being underrated, I think it was quite overlooked some time ago, but it's got some recognition during the last years, though Sgt. Pepper's and Revolver are still the most acclaimed Beatles albums.