Nadal hasn't captured the imagination of fans as Fed and Djok have. It's natural in sport (although not as much in today's tennis) for fans of one player to resent the other (although Djokovic/Nadal fans are not uncommon at all). It's due to his humble, reserved, un-Hollywood personality (Djokovic and Federer are always the center of attention, but Nadal is much more down-to-earth) and his playstyle (he doesn't go for the flashy stuff and his game isn't as aesthetically pleasing as Federer's fluidity or Djokovic's accuracy; Nadal prefers to scrap and bullfight his way through. To his fans (and me), that is the most admirable trait.
But I would bet that in 20 years, the most talked-about player will be Nadal; how he revolutionized the game and forced his competition to work even harder, and how he played through pain, and suffered for the title as nobody had done before. Similarly, in the late 80's, the most popular players were Edberg and Becker. Their tennis was more exciting to watch than the grinding baseline game of the stoic, robot-like No.1 Lendl. Lendl was one of the least loved top players, and was often rooted against. Fast forward 30 years. While Edberg and Becker are still popular and well-remembered today, they aren't credited with revolutionizing the game and creating the baseline tennis that has dominated ever since. That award, as well as the most important player of the time period, without doubt, goes to Ivan Lendl.
So don't worry if Nadal is underappreciated, disliked, and rooted against today. He will be remembered for a very long time, and his impact on the game may last much longer than that of Federer and Djokovic.