If you look at Rob Galbraith's tests it's clear that SD is quicker, by up to 15% or so (Extreme III SD v Extreme IV CF). Capacity isn't that much of an issue, most people prefer to go with multiple smaller cards than one large one. Price is a non issue as well, just had a quick check and 2Gb of Extreme III CF was £83, 2Gb of Extreme III SD was only £76.
On top of that SD is smaller and has a more reliable mechanical interface.
On top of that SD is smaller and has a more reliable mechanical interface.