Theoretically, every champion's Win Rate should be 50%. Realistically, achieving that is nearly impossible (and we don't want it anyway; perfect balance != everything is identical).
Win Rate is merely a champions number of wins divided by how many games they are played in. Plain and simple. Most Win Rate statistics you find online (such as those on LoLKing) are calculated for a recent time period in order to give you an idea of recent performance. Win Rate stats do NOT account for the popularity of a champion (aka Pick Rate). There are several patterns that can typically be observed by comparing combinations of these statistics. A high Popularity (approximately 10 / 123 = 8% is average, so anything over 20% can safely be considered high) can happen in several scenarios, but is always based on at least the perception of power.
If high Popularity coincides with a very high Win Rate, it's reasonable to assume that the champion in question is overtuned, and needs a few significant nerfs to their numbers. Extreme cases such as a Win Rate of 55% or higher need immediate attention if the champion in question is highly popular.
On the other hand, there are also cases where a champion is highly popular, but has a poor Win Rate. This typically means that the champion is A) new or B) perceived to be very powerful. In both of these cases, the poor Win Rate if often due to a great number of inexperienced players hopping on the bandwagon, greatly skewing the Win Rate.
In the long-term, this tends to settle down some, but it does not go away entirely. If the champion is difficult to play, the trend will remain. Take a look at Lee Sin, for example. There are a great many posts made about how Lee Sin is "OP" (I'm not offering my opinion either way; another time perhaps =P), yet his current Win Rate is only 46.68%. Lee Sin is incredibly versatile and dangerous in the right hands, but he requires a fairly high level of skill in order to properly take advantage of this. Well over half of the playerbase does not possess the necessary level of skill to use him well, but that does not stop them trying anyway because "WOW, LEE SIN OP! DID YOU SEE THAT STREAM LAST NIGHT OMG #LCSBIGPLAYS!"
Win Rate is a great statistic, but has to be taken with a grain of salt; there are a great many factors that go into it, and just looking at the end result doesn't give you a very clear picture.