I think its all in your head.
If you look at the websites for counter picks they select counter picks 1 of 2 ways:
1) Statistically: When a champion dies (what opposing champion got the KB)
If you think about it though, it takes no account of the opposing players skill, nor the actual damage done by the opposing champion. (Meaning the champion COULD be just be good at KSing)
2) By user votes: Meaning anyone registered as a user of that site can vote who they think counters that champion.
Thats purely opinion based, and the people could range from noob to pro... but all votes weigh the same.
Neither system has a way of weighing statistics/votes with addition of new champs. (Meaning that the votes or stats are always going to be weighted toward older champions)
Naturally you are going to have poor match ups (in lane)... ranged vs a melee champion.
It would not appear that either system differentiates between normal mode, and dominion (which DOES change things IMO)
So whats your opinion... or what do you know that I don't?
I think its all hokum! Some of you may revere counter picks as biblical truth.