I don't know why people think that NCAA Tourney results determine whether a conferences strength is over/under rated. Maybe if all games were best of five but one-off games mean little. Conference strength is determined before the tourney starts--the number of (or percentage) of teams and their respective seed line is more indicative.
The results shouldn't be completely thrown out, but basing the conference strength entirely on it shouldn't happen either. The Big 12 metrically was by far the strongest conference all year long. Towards the end of the year though, and it's been brought up, teams had injuries that plagued them and it showed in the tournament.
Matchups also play a huge factor into things. A depleted KU gets Gonzaga in the second round, Iowa State is playing on the toughest side of the bracket, a team like Texas Tech pulling in the first round a team who ends up being the hottest team in the country, etc.