I don't see any difference in RIM charging for CALs versus Microsoft or IBM for Exchange and Notes CALs, respectively. Its just another way to be profitable off your product. Considering licensing programs are one of the primary sources of income for a long-term profitability model, I think this is fairly smart. Where I do see an issue is with their support programs now being based on BES plus total number of handhelds rather than one ballooned figure for all aspects of the BES.
But yes, $99 is the price for an individual CAL. Of course, you can usually get this at around $80 from other non-RIM outlets (or even cheaper on eBay, etc), as well as cheaper per CAL pricing when purchased in bulk (somewhere near $50/ea for 100). For Corporate America, if BlackBerry has been justified as a profitability tool for decision makers or anyone else, this CAL fee is not that viewed as much overhead in the grand scheme of things; although with smaller companies, I can see how this would amass to seemingly unnecessary extra fees forced down by a money-hungry giant.
..or something along those lines