I think in order for a civ to qualify as underrated, most people would have to think they suck. It also depends on whether you're talking multiplayer or singleplayer, Deity or Prince.
I constantly hear people say that Denmark, India and Polynesia are terrible. I think, as usual, what that really means is that you have to adjust your play style. Denmark is incredibly effective at surprise attack. Polynesia's ability to explore the whole map super-early is very useful. India's UA for doubling unhappiness from number of cities actually makes them *better* at going wide, not worse, in the long run, as long as you're not talking ICS.
(Base 6 unhappiness per city instead of base 3, but with ten 10-pop cities, that's 50 unhappiness from population and 60 from number of cities, instead of 100 from population and 30 from number of cities, for 20 *LESS* unhappiness)
So, they just require you change your playstyle, that's all. There are however, civs, IMHO, despite what Tommy says, that are just noticeably superior because of the synergy between their UA/UU/UB and the tech/policy trees. Notably, the Inca get terrace farms at Construction, which, on Deity at least, is very, very nice, because you tend to want to rush to Construction anyway. Cheap roads and fast movement in hills is tremendously useful. They're effective at both conquest and turtle. Poland's free policies are useful no matter your end goal. But a lot of UAs are not nearly as generically useful.
Denmark gets their UU at Machinery, and their UA only gives benefit if you go Domination, and to take advantage of all that you have to go with a very non-standard tech plan. You have to go all-in on Iron and Siege, and unlike say, Arabia, you don't get Civil Service en route to your UU, which really hurts for growth and tech in the long run because unless you win by t160, you're screwed. So, there are definitely civs that are harder to win with, unquestionably. IMHO.
You could also say that Polynesia, Indonesia, Denmark aren't under-rated, just *harder to use*. But IMHO that means they're not under-rated. They're rated exactly where they should be. The easier civs to win with are better. /shrug
However, of those three, Denmark is the one that jumps out to me as being *incredibly effective* when used correctly. Even Pangaea has a lot of coastline most times. Sometimes TOO much if you ask me, but whatever.