I too have no problems with the increased fees.
I thought these stats from the document were very interesting:
Non-commercial permits for the high-use river season (April through October) are initially distributed through a lottery that occurs the first week of February. Successful applicants receive a launch reservation, which they must confirm and pay for within 30 days of their launch date to obtain a river permit. Each year the Monticello Field Office receives approximately 4,200 noncommercial applications for the permit lottery. There is currently no fee to apply. In 2011, 90% or 3,695 applications were submitted for launches during the peak user demand season of April 15th through July 15th. Of the applications submitted for April 15th through July 15th, 12% were successfully drawn. Applications submitted for launch dates outside of April 15th through July 15th, had a 75% success rate. Unsuccessful applicants, as well as applicants who apply for a permit following the lottery, can then obtain available and cancelled permits through advance phone reservations. In 2011, the majority of private river users (62%) obtained their permit through post-lottery phone reservations and cancellations, rather than the lottery.
The vast majority of private use is regional. In 2011, 86% of private permits were issued to trip leaders from the four corners states (Utah, Colorado, Arizona, and New Mexico). 46% of private permits were issued to trip leaders who reside in Colorado. 25% of private permits were issued to trip leaders from the communities of Durango, CO (15%) and Flagstaff, AZ (10%). Less than 1% were issued to local (San Juan County, UT) or international boaters. The visitor origin of all private river runners is likely more widespread than that of the permitted trip leaders, as many trip leaders bring visiting family and friends from beyond the region.