Conferences cheer for their conference. Atleast the smaller ones do. As a former MAC athlete I will always cheer for MAC teams when they play any school from any other conference (except maybe WMU

). It always reflects well on your conference when they beat a team from a different conference. When a Big T11n school gets beat by a MAC school it looks great for everyone not just the team who won.
Ask Boise or TCU fans the same thing about WAC or Mountain West teams beating BCS opponents and whether not it reflects well on the conference.