If a coin lands on head 56% of the time after 300 000 tries, then something is wrong with the coin. It's all about sample. If a champion with a high popularity also has a high winrate, that champ is just stronger than others. On top of this, high popularity means that the champ is probably being picked up BECAUSE of its power by players who don't have a clue how to play them because they're not dedicated to them which lowers the winrate. If the winrate is still high, it means their actual power is even higher! Also, low winrate often means that the champ is usually played as a counterpick only.
For example: Trundle has the highest winrate of all supports. Is he OP? No. He's played in only 0.48% of the games. Blitzcrank and Janna have a slightly lower winrate, but they're played 16% and 21% of the time respectively. This difference in popularity can mean 3 things.
- Trundle is a niche pick that works with certain comps/against certain champs and rarely picked in a random situation.
- Janna/Blitzcrank are stronger than their winrate suggests, but a lot of players with low experience started to play them because they seem strong.
- The winrate of Trundle is rather unreliable because the sample size is only 540 games opposed to 18k and 23k games of Blitz and Janna.
In the meanwhile, the most popular support champ is Thresh, while his winrate is only 49%. Does this mean he's bad? Well, the same thing that counted for janna and blitz count even more for thresh: Lot's of people just play him because "thresh OP rite?" who lower the succesrate of the champion. However, Winrate still does matter. The fact that Thresh is only at 49% opposed to 53+% is a big deal. A difference of 4% winrate over the course of 20k games is a difference of 800 games won. If you as a player have 54% winrate over the course of 20k games in one season, you're #1 challenger.