Why are many Universities against a College Football Playoff?
After LSU's victory last night, we appear to be heading towards a split national championship. If there had been a playoff system in lieu of the bowl system that we have now, this would not be an issue, however there has been historic resistance to the idea, notwithstanding the recent effort by several college presidents to pressure the BCS via congress and antitrust threats. CNN money has a slightly dated article that provides some background on the matter

Key quote -
The 63 schools in the BCS not only keep $111.4 million of the $118 million paid out by the four big-money BCS bowls -- the Rose, Fiesta, Sugar and Orange bowls -- they also get the lion's share of the rest of the money -- about $53 million for grabbing 32 of the 48 spots open in the non-BCS bowls.

That leaves crumbs -- about $14 million to be spread among the other 54 1A schools not in the BCS conferences in order to have 16 teams from those conferences go to bowls, plus about $4.5 million that those conferences get from BCS.

However, perhaps there is something else at play too - as another article by the author alludes to

Key quote
But the real force against a playoff is that teams, which know they will likely never play for a championship, feel it's in their interest to maintain the wide range of secondary bowls. There are enough bowls today that most teams with a winning record can get a bowl bid. There is a strong, probably justifiable fear that most of these lesser bowls would disappear if the BCS or National Collegiate Athletic Association were to set up a playoff system. And these second-tier football programs control the various conferences through their sheer numbers.

"A playoff would be disastrous for the (other) bowls," said Trangese. "The bowl system is not going away. It's too valuable to us."

Going to a bowl is important to a lot of schools that won't make the top bowls for other reasons as the second article later implies

But the football programs that have suffered through a 6-5 or 7-4 season feel they need to have a bowl bid as a way to thank staff and players, satisfy and woo alumni, and recruit future players.