Why not? Not every team that won a national championship would be ranked as one of the 64 greatest ever. You have to take into account massive favourites that got beat ('75 Indiana, '83 Houston, '85 Georgetown, '91 UNLV) and teams that never even played in the tournament (I think I read that '54 Kentucky ended the season at No. 1 but declined a NCAA tournament bid, at a time when the NIT was more prestigious).
The whole exercise was ridiculous, though. Most of the voters have never seen the great UCLA teams, let alone heard of the dominant USF teams with Bill Russell. Anything older than 25 years ago is dismissed, as is anything without a household name (which is why '76 Indiana didn't trounce '82 UNC -- "How the hell is Quinn Buckner going to beat MJ and Worthy?")