For me, championships are the highest prize in a respective sport, only to be earned by the best teams competing against each other after having proved themselves worthy throughout a season.
What I can't stand about basketball is how I can follow a handful of teams all year long who are dominant, only to get beat in the second round of the Tourney because some bubble team got hot and hit a bunch of 3s that lead to an upset. When this happens, it inadvertently punishes the team who's merits suggest they're far better than that given day would suggest. Bye bye championship.
For some, the above scenario is exactly what makes it all so exciting. I agree; it is exciting. But is the goal to be entertained, or is it to ultimately crown the best team? TV execs have us all believing it's the former.
The only logical argument I've been able to tell myself is that it's okay to not view it in a vacuum. For example, crowning a conference champion rewards the merits of the regular season. Crowning a national champion rewards the merits of a tournament of champions in the post season. This is why I, myself, have backed away from the standard models and became okay with tournament expansion to 12 teams (although, I would've preferred only 8).