Elite athletes are not like most of us. The best of them have a certain drive that allows them to train harder, faster, and longer than the average. But many people can train hard. Elite athletes are also born with physical attributes that make them different than average people. Bigger lung capacity, unusually proportioned limbs, better eyesight or hand-eye coordination.
Elite swimmers have many of these attributes (maybe not the eyesight), but one thing that many of them also have in common is joint flexibility. Joint flexibility allows better leverage and better grip on the water, longer strokes, and stronger kicks. In particular, hyperextendable knees allow more depth on the kicks for all but the breaststroke - elite breaststrokers have other physical advantage.
The linked Daily Mail article has several pictures of Olympic medalist and world record holder Ryan Lochte. He's obviously strong and tall and developed (though a little post-Olympic soft). But in the first picture, notice how hyperextended his knee is. That's a physical trait he was born with, which gives him a stronger kick. Next time you watch a world-class swim meet (if you do), notice how many of the competitors also have hyperextendable knees. It's something you can't win without.