The real test of the negative effect CHAN matches will have on the ranking of CAF teams will come when the CHAN tournament is over, and we see the movement in the ranking. So far, only qualifiers and friendlies have been included. If previous CHAN results are anything to go by, it will totally screw up the position of the African teams. The Top 4 from the 2011 tournament were Tunisia/Angola/Sudan/Algeria. In 2009, DR Congo won the tournament, and hosts Ivory Coast lost 0-1 to Tanzania, 0-3 to Zambia and drew 0-0 with Senegal. These 3 match results would have had a horrendous effect on Ivory Coast's ranking if they'd been included. Also, half of the time, the CHAN friendly matches are not official, because the FAs do not notify CAF or FIFA (because, clearly, they don't think they need to, or they don't class them as 'A' international matches themselves). So we have a situation where there is no difference at all between the status of these friendly matches, but only the select few who notify CAF get their matches included.
Anyway - FIFA made the decision based on idiotic logic. On their heads be it.