No, I don't think Rubber Soul is underrated. I do think it is a tad overrated, though. To me, I think the three masterpiece albums were Revolver, The White Album, and Abbey Road. I still think Rubber Soul is a great album, but it does confuse me when it outranks some of those titles. And I think it is a little strange that RS had 6 songs on the Red Album, and Revolver only 2! Also, Sgt. Pepper had 4 songs on the Blue album, Abbey Road had 4, and the White Album only had 3.
Well, I think the good thing about the Beatles' career is that they don't have one album that is universally considered to be their best, as opposed to, let's say the Beach Boys. Look at any poll. I would say 90% of the time, the top 5 Beatles albums are the same 5 titles, just in a different order.
However, if it is any consolation, an argument in favour of Rubber Soul being underrated is that it is the only album from the Beatles' top five that I don't think I have ever seen ranked as the top Beatles album.