How much do you want/value the upgrade? This is what its about. Paying to guarantee an upgrade vs. playing the free upgrade game.

You won this time, but very well may lose next time (Yes - I understand you knowing how many F seats are left for sale gives you a bit better insight into your odds). For some people, sitting in coach isn't a big deal, and others might be hitting themselves on the head for declining a $99 upgrade offer, and then subsequently finding out that they didn't get a CPU. For the latter group, $99 may very well have been money well spent, whether or not an upgrade was coming their way anyway.