We used to use cruise line air but stopped doing so several years ago, and for all the reasons mentioned.
Now that I've told you that, I need to admit that for my 3-night cruise out of Port Canaveral this August I am using Royal Caribbean's air. Two reasons - the price in this particular instance is the same when you throw the transfers in, and the cruise line already has me on direct flights from HSV to MCO (Huntsville to Orlando) and also on the return home. (I called Custom Air to fine tune my flights today and was surprised they had selected the flights that I wanted without my asking.)
Note that the key here is direct flights. If that option wasn't available I more than likely would have done my own air. It just so happens that we have two direct flights in both directions every day.
It is also true that in most cases the cruise line air is more expensive, but lately it isn't as true as it used to be given the airline woes.