NCAA college eligibility is probably the biggest reason. The NCAA considers the three member leagues of the Canadian Hockey League (the WHL, OHL and QMJHL) to be professional, so any player who suits up in one of these leagues is deemed ineligible to play NCAA hockey. Kids that play Junior A hockey retain this eligibility, and there is a growing trend of players going from Junior A to NCAA to the NHL (i.e.: Dany Heatley) rather than CHL to NHL.
The WHL has its own scholarship program, however, offering one full year's tuition for every year played in the WHL. The CIS places no restrictions on the eligibility of CHL graduates.