Yes employers are allowed to weigh one university over another in terms of not only their accreditation but also their reputation.
If two (identical candidates) apply for a position and one has a business degree from Harvard while the other has one from University of Phoenix or Westwood College, the odds are the Harvard Grad will get the position.
Some schools strictly fall under the "for profit" banner. They don't invest a lot of time and money attempting to reach national accreditation standards. It's pretty much up to the would be student to do the research.
To be on the safe side one can always pursue well known state and privately run schools. General rule of thumb if your college runs TV and radio ads during the day and post ads in newspapers as well as Internet banners with a 800# it's probably not as respected as Indiana University, Stanford, UCLA, Ohio State, and the like.
If the school curriculum is designed with one class per month or is primarily "online" it also isn't likely to garner the same respect.
However many other factors also come into play such as the candidate's personality and how well they interviewed. When it's all said and done most managers hire people they like and feel would get along with others on their team. Having the right degree just gets you in the door. You still have to sell yourself.