You probably don't even know that prior to '75 (the end of the UCLA dynasty, btw), the tourney only included one team per conference. Teams that were ranked #2 or 3 in the nation or went undefeated in conference play were left out.
Nevermind that over 40 years of basketball were played before the NCAA tourney began, or that the field has evolved from 8 to 68 teams.
Then you have the fact that the NIT was at one time the prominent tourney, and some years neither tourney had clear dominance. For example, in 1948, Kentucky won the NCAA tournament, while the #2, 4, 5, 6 and 7th ranked teams played in the NIT.
Then you have the fact that the game evolved into keep-away for a long stretch before the shot clock era, taking away the advantage of superior athletes/skilled players.
Just a few reasons why determining the top programs over 120 years by NCAA titles alone is for simpletons.