Inca were seen as the best generalist Civ. Well, they
were before Poland was added to the game
. The boost in food, hammers, and gold give an all-around strong empire to go after any of the victory types.
Underrated may not be the correct term... more just ignored, but I will throw out Austria. CS bonuses scale rather poorly come mid to late game (when you are actually purchasing CS's). A Maritime's +1 food on your secondary cities is a rather weak incentive to keep it as an ally.
The overall pros far outweigh the cons IMO.
--Austria is one of the few Civs which can "expand" in mid game and still benefit from it. Most everyone else settles their core cities early on and stick with those until the end. It takes too long for later settled cities to catch up. Not with Austria. You start with a decent population and many of the core buildings already finished.
--You get easy access to naval units. CS's love spamming naval units. This is potentially important, because when you unlock frigates/privateers you are often too busy trying to get up schools and factories or trying to win World's Fair to try and pump out a navy. And once you have them, it is just as easy to keep them upgraded to battleships/destroyers.
--There is typically one dominant CS-hoarder who starts buying up all the CS's towards the second half of the game. If you get early rep from a quest or one time purchase gold dump, you can remove that CS from the game ensuring that same CS-hoarder has less dominant control over WC, can't declare war and flip CS aggression as easily, etc.
The major con for Austria is they are basically forced into either a domination win or science win. It is easy to understand why they are ignored, since their domination perks tend to be focused towards mid and late game, and people would rather clear a map with horse archers than wait that long. For science, a lot of people prefer the straight up, clear, easy to read bonuses of extra science on specialists for Korea, as opposed to Austria's indirect late-game increase bulk science rate through mass horizontal growth for ridiculous GS bulbs. Despite those reasons, Austria performs surprisingly well on both fronts.