Nope, you are mistaking...
The MASAC and NE champs will have earned it by winning the conference tournament of a league that meets the NCAA criteria for an autobid. Period.
Atlantic Hockey's champ gets an AQ at the D1 level and occasionally makes some noise (see RIT and Holy Cross.). The Underdog/Hoosiers element is one of the cool things about NCAA hockey and if you don't like that, then beat it, you're following the wrong sport.
Just relax, it looks like there is a good possibility that the W is going to get a 7th member and an AQ fairly soon, and the team you follow will have its fair shot at a Pool A too.