The number of refs is decided by the host school. Some schools always have 3 refs, they tend to be the ones that have large fan support. Others only have 2 refs becuase they cannot afford to pay for the 3rd referee. If fans aren't coming to the game, no ticket sales are generated, and thus lack of funds to pay for officials.
Some coaches look at thier schedule and determine that certain games will require a 3rd set of eyes and request a 3rd ref for just certain matches (ie. a match that may determine the region champion, a heated rivalry match, etc...).
Bottom line, refs cost money. Some schools have money to afford 3, others have barely enough money to sponsor a team and can barely afford 2 refs. I have never met a coach that said they would always like to have 2 refs. 3 is ideal, but not always economical.